diff --git a/.buildkite/postgres-config.yaml b/.buildkite/postgres-config.yaml
index a35fec394d..2acbe66f4c 100644
--- a/.buildkite/postgres-config.yaml
+++ b/.buildkite/postgres-config.yaml
@@ -1,7 +1,7 @@
 # Configuration file used for testing the 'synapse_port_db' script.
 # Tells the script to connect to the postgresql database that will be available in the
 # CI's Docker setup at the point where this file is considered.
-server_name: "test"
+server_name: "localhost:8800"
 
 signing_key_path: "/src/.buildkite/test.signing.key"
 
diff --git a/.buildkite/sqlite-config.yaml b/.buildkite/sqlite-config.yaml
index 635b921764..6d9bf80d84 100644
--- a/.buildkite/sqlite-config.yaml
+++ b/.buildkite/sqlite-config.yaml
@@ -1,7 +1,7 @@
 # Configuration file used for testing the 'synapse_port_db' script.
 # Tells the 'update_database' script to connect to the test SQLite database to upgrade its
 # schema and run background updates on it.
-server_name: "test"
+server_name: "localhost:8800"
 
 signing_key_path: "/src/.buildkite/test.signing.key"
 
diff --git a/changelog.d/6487.misc b/changelog.d/6487.misc
new file mode 100644
index 0000000000..18b49b9cbd
--- /dev/null
+++ b/changelog.d/6487.misc
@@ -0,0 +1 @@
+Pass in `Database` object to data stores.
diff --git a/scripts/synapse_port_db b/scripts/synapse_port_db
index 72061177c9..e393a9b2f7 100755
--- a/scripts/synapse_port_db
+++ b/scripts/synapse_port_db
@@ -55,6 +55,7 @@ from synapse.storage.data_stores.main.stats import StatsStore
 from synapse.storage.data_stores.main.user_directory import (
     UserDirectoryBackgroundUpdateStore,
 )
+from synapse.storage.database import Database
 from synapse.storage.engines import create_engine
 from synapse.storage.prepare_database import prepare_database
 from synapse.util import Clock
@@ -139,39 +140,6 @@ class Store(
     UserDirectoryBackgroundUpdateStore,
     StatsStore,
 ):
-    def __init__(self, db_conn, hs):
-        super().__init__(db_conn, hs)
-        self.db_pool = hs.get_db_pool()
-
-    @defer.inlineCallbacks
-    def runInteraction(self, desc, func, *args, **kwargs):
-        def r(conn):
-            try:
-                i = 0
-                N = 5
-                while True:
-                    try:
-                        txn = conn.cursor()
-                        return func(
-                            LoggingTransaction(txn, desc, self.database_engine, [], []),
-                            *args,
-                            **kwargs
-                        )
-                    except self.database_engine.module.DatabaseError as e:
-                        if self.database_engine.is_deadlock(e):
-                            logger.warning("[TXN DEADLOCK] {%s} %d/%d", desc, i, N)
-                            if i < N:
-                                i += 1
-                                conn.rollback()
-                                continue
-                        raise
-            except Exception as e:
-                logger.debug("[TXN FAIL] {%s} %s", desc, e)
-                raise
-
-        with PreserveLoggingContext():
-            return (yield self.db_pool.runWithConnection(r))
-
     def execute(self, f, *args, **kwargs):
         return self.db.runInteraction(f.__name__, f, *args, **kwargs)
 
@@ -512,7 +480,7 @@ class Porter(object):
 
         hs = MockHomeserver(self.hs_config, engine, conn, db_pool)
 
-        store = Store(conn, hs)
+        store = Store(Database(hs), conn, hs)
 
         yield store.db.runInteraction(
             "%s_engine.check_database" % config["name"], engine.check_database,
diff --git a/synapse/app/federation_sender.py b/synapse/app/federation_sender.py
index 448e45e00f..f24920a7d6 100644
--- a/synapse/app/federation_sender.py
+++ b/synapse/app/federation_sender.py
@@ -40,6 +40,7 @@ from synapse.replication.slave.storage.transactions import SlavedTransactionStor
 from synapse.replication.tcp.client import ReplicationClientHandler
 from synapse.replication.tcp.streams._base import ReceiptsStream
 from synapse.server import HomeServer
+from synapse.storage.database import Database
 from synapse.storage.engines import create_engine
 from synapse.types import ReadReceipt
 from synapse.util.async_helpers import Linearizer
@@ -59,8 +60,8 @@ class FederationSenderSlaveStore(
     SlavedDeviceStore,
     SlavedPresenceStore,
 ):
-    def __init__(self, db_conn, hs):
-        super(FederationSenderSlaveStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(FederationSenderSlaveStore, self).__init__(database, db_conn, hs)
 
         # We pull out the current federation stream position now so that we
         # always have a known value for the federation position in memory so
diff --git a/synapse/app/homeserver.py b/synapse/app/homeserver.py
index 9f81a857ab..df65d0a989 100644
--- a/synapse/app/homeserver.py
+++ b/synapse/app/homeserver.py
@@ -68,9 +68,9 @@ from synapse.rest.key.v2 import KeyApiV2Resource
 from synapse.rest.media.v0.content_repository import ContentRepoResource
 from synapse.rest.well_known import WellKnownResource
 from synapse.server import HomeServer
-from synapse.storage import DataStore, are_all_users_on_domain
+from synapse.storage import DataStore
 from synapse.storage.engines import IncorrectDatabaseSetup, create_engine
-from synapse.storage.prepare_database import UpgradeDatabaseException, prepare_database
+from synapse.storage.prepare_database import UpgradeDatabaseException
 from synapse.util.caches import CACHE_SIZE_FACTOR
 from synapse.util.httpresourcetree import create_resource_tree
 from synapse.util.manhole import manhole
@@ -294,22 +294,6 @@ class SynapseHomeServer(HomeServer):
             else:
                 logger.warning("Unrecognized listener type: %s", listener["type"])
 
-    def run_startup_checks(self, db_conn, database_engine):
-        all_users_native = are_all_users_on_domain(
-            db_conn.cursor(), database_engine, self.hostname
-        )
-        if not all_users_native:
-            quit_with_error(
-                "Found users in database not native to %s!\n"
-                "You cannot changed a synapse server_name after it's been configured"
-                % (self.hostname,)
-            )
-
-        try:
-            database_engine.check_database(db_conn.cursor())
-        except IncorrectDatabaseSetup as e:
-            quit_with_error(str(e))
-
 
 # Gauges to expose monthly active user control metrics
 current_mau_gauge = Gauge("synapse_admin_mau:current", "Current MAU")
@@ -357,16 +341,12 @@ def setup(config_options):
 
     synapse.config.logger.setup_logging(hs, config, use_worker_options=False)
 
-    logger.info("Preparing database: %s...", config.database_config["name"])
+    logger.info("Setting up server")
 
     try:
-        with hs.get_db_conn(run_new_connection=False) as db_conn:
-            prepare_database(db_conn, database_engine, config=config)
-            database_engine.on_new_connection(db_conn)
-
-            hs.run_startup_checks(db_conn, database_engine)
-
-            db_conn.commit()
+        hs.setup()
+    except IncorrectDatabaseSetup as e:
+        quit_with_error(str(e))
     except UpgradeDatabaseException:
         sys.stderr.write(
             "\nFailed to upgrade database.\n"
@@ -375,9 +355,6 @@ def setup(config_options):
         )
         sys.exit(1)
 
-    logger.info("Database prepared in %s.", config.database_config["name"])
-
-    hs.setup()
     hs.setup_master()
 
     @defer.inlineCallbacks
diff --git a/synapse/app/user_dir.py b/synapse/app/user_dir.py
index b6d4481725..c01fb34a9b 100644
--- a/synapse/app/user_dir.py
+++ b/synapse/app/user_dir.py
@@ -43,6 +43,7 @@ from synapse.replication.tcp.streams.events import (
 from synapse.rest.client.v2_alpha import user_directory
 from synapse.server import HomeServer
 from synapse.storage.data_stores.main.user_directory import UserDirectoryStore
+from synapse.storage.database import Database
 from synapse.storage.engines import create_engine
 from synapse.util.caches.stream_change_cache import StreamChangeCache
 from synapse.util.httpresourcetree import create_resource_tree
@@ -60,8 +61,8 @@ class UserDirectorySlaveStore(
     UserDirectoryStore,
     BaseSlavedStore,
 ):
-    def __init__(self, db_conn, hs):
-        super(UserDirectorySlaveStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(UserDirectorySlaveStore, self).__init__(database, db_conn, hs)
 
         events_max = self._stream_id_gen.get_current_token()
         curr_state_delta_prefill, min_curr_state_delta_id = self.db.get_cache_dict(
diff --git a/synapse/replication/slave/storage/_base.py b/synapse/replication/slave/storage/_base.py
index 6ece1d6745..b91a528245 100644
--- a/synapse/replication/slave/storage/_base.py
+++ b/synapse/replication/slave/storage/_base.py
@@ -20,6 +20,7 @@ import six
 
 from synapse.storage._base import SQLBaseStore
 from synapse.storage.data_stores.main.cache import CURRENT_STATE_CACHE_NAME
+from synapse.storage.database import Database
 from synapse.storage.engines import PostgresEngine
 
 from ._slaved_id_tracker import SlavedIdTracker
@@ -35,8 +36,8 @@ def __func__(inp):
 
 
 class BaseSlavedStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(BaseSlavedStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(BaseSlavedStore, self).__init__(database, db_conn, hs)
         if isinstance(self.database_engine, PostgresEngine):
             self._cache_id_gen = SlavedIdTracker(
                 db_conn, "cache_invalidation_stream", "stream_id"
diff --git a/synapse/replication/slave/storage/account_data.py b/synapse/replication/slave/storage/account_data.py
index bc2f6a12ae..ebe94909cb 100644
--- a/synapse/replication/slave/storage/account_data.py
+++ b/synapse/replication/slave/storage/account_data.py
@@ -18,15 +18,16 @@ from synapse.replication.slave.storage._base import BaseSlavedStore
 from synapse.replication.slave.storage._slaved_id_tracker import SlavedIdTracker
 from synapse.storage.data_stores.main.account_data import AccountDataWorkerStore
 from synapse.storage.data_stores.main.tags import TagsWorkerStore
+from synapse.storage.database import Database
 
 
 class SlavedAccountDataStore(TagsWorkerStore, AccountDataWorkerStore, BaseSlavedStore):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         self._account_data_id_gen = SlavedIdTracker(
             db_conn, "account_data_max_stream_id", "stream_id"
         )
 
-        super(SlavedAccountDataStore, self).__init__(db_conn, hs)
+        super(SlavedAccountDataStore, self).__init__(database, db_conn, hs)
 
     def get_max_account_data_stream_id(self):
         return self._account_data_id_gen.get_current_token()
diff --git a/synapse/replication/slave/storage/client_ips.py b/synapse/replication/slave/storage/client_ips.py
index b4f58cea19..fbf996e33a 100644
--- a/synapse/replication/slave/storage/client_ips.py
+++ b/synapse/replication/slave/storage/client_ips.py
@@ -14,6 +14,7 @@
 # limitations under the License.
 
 from synapse.storage.data_stores.main.client_ips import LAST_SEEN_GRANULARITY
+from synapse.storage.database import Database
 from synapse.util.caches import CACHE_SIZE_FACTOR
 from synapse.util.caches.descriptors import Cache
 
@@ -21,8 +22,8 @@ from ._base import BaseSlavedStore
 
 
 class SlavedClientIpStore(BaseSlavedStore):
-    def __init__(self, db_conn, hs):
-        super(SlavedClientIpStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SlavedClientIpStore, self).__init__(database, db_conn, hs)
 
         self.client_ip_last_seen = Cache(
             name="client_ip_last_seen", keylen=4, max_entries=50000 * CACHE_SIZE_FACTOR
diff --git a/synapse/replication/slave/storage/deviceinbox.py b/synapse/replication/slave/storage/deviceinbox.py
index 9fb6c5c6ff..0c237c6e0f 100644
--- a/synapse/replication/slave/storage/deviceinbox.py
+++ b/synapse/replication/slave/storage/deviceinbox.py
@@ -16,13 +16,14 @@
 from synapse.replication.slave.storage._base import BaseSlavedStore
 from synapse.replication.slave.storage._slaved_id_tracker import SlavedIdTracker
 from synapse.storage.data_stores.main.deviceinbox import DeviceInboxWorkerStore
+from synapse.storage.database import Database
 from synapse.util.caches.expiringcache import ExpiringCache
 from synapse.util.caches.stream_change_cache import StreamChangeCache
 
 
 class SlavedDeviceInboxStore(DeviceInboxWorkerStore, BaseSlavedStore):
-    def __init__(self, db_conn, hs):
-        super(SlavedDeviceInboxStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SlavedDeviceInboxStore, self).__init__(database, db_conn, hs)
         self._device_inbox_id_gen = SlavedIdTracker(
             db_conn, "device_max_stream_id", "stream_id"
         )
diff --git a/synapse/replication/slave/storage/devices.py b/synapse/replication/slave/storage/devices.py
index de50748c30..dc625e0d7a 100644
--- a/synapse/replication/slave/storage/devices.py
+++ b/synapse/replication/slave/storage/devices.py
@@ -18,12 +18,13 @@ from synapse.replication.slave.storage._slaved_id_tracker import SlavedIdTracker
 from synapse.replication.tcp.streams._base import DeviceListsStream, UserSignatureStream
 from synapse.storage.data_stores.main.devices import DeviceWorkerStore
 from synapse.storage.data_stores.main.end_to_end_keys import EndToEndKeyWorkerStore
+from synapse.storage.database import Database
 from synapse.util.caches.stream_change_cache import StreamChangeCache
 
 
 class SlavedDeviceStore(EndToEndKeyWorkerStore, DeviceWorkerStore, BaseSlavedStore):
-    def __init__(self, db_conn, hs):
-        super(SlavedDeviceStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SlavedDeviceStore, self).__init__(database, db_conn, hs)
 
         self.hs = hs
 
diff --git a/synapse/replication/slave/storage/events.py b/synapse/replication/slave/storage/events.py
index d0a0eaf75b..29f35b9915 100644
--- a/synapse/replication/slave/storage/events.py
+++ b/synapse/replication/slave/storage/events.py
@@ -31,6 +31,7 @@ from synapse.storage.data_stores.main.signatures import SignatureWorkerStore
 from synapse.storage.data_stores.main.state import StateGroupWorkerStore
 from synapse.storage.data_stores.main.stream import StreamWorkerStore
 from synapse.storage.data_stores.main.user_erasure_store import UserErasureWorkerStore
+from synapse.storage.database import Database
 
 from ._base import BaseSlavedStore
 from ._slaved_id_tracker import SlavedIdTracker
@@ -59,13 +60,13 @@ class SlavedEventStore(
     RelationsWorkerStore,
     BaseSlavedStore,
 ):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         self._stream_id_gen = SlavedIdTracker(db_conn, "events", "stream_ordering")
         self._backfill_id_gen = SlavedIdTracker(
             db_conn, "events", "stream_ordering", step=-1
         )
 
-        super(SlavedEventStore, self).__init__(db_conn, hs)
+        super(SlavedEventStore, self).__init__(database, db_conn, hs)
 
     # Cached functions can't be accessed through a class instance so we need
     # to reach inside the __dict__ to extract them.
diff --git a/synapse/replication/slave/storage/filtering.py b/synapse/replication/slave/storage/filtering.py
index 5c84ebd125..bcb0688954 100644
--- a/synapse/replication/slave/storage/filtering.py
+++ b/synapse/replication/slave/storage/filtering.py
@@ -14,13 +14,14 @@
 # limitations under the License.
 
 from synapse.storage.data_stores.main.filtering import FilteringStore
+from synapse.storage.database import Database
 
 from ._base import BaseSlavedStore
 
 
 class SlavedFilteringStore(BaseSlavedStore):
-    def __init__(self, db_conn, hs):
-        super(SlavedFilteringStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SlavedFilteringStore, self).__init__(database, db_conn, hs)
 
     # Filters are immutable so this cache doesn't need to be expired
     get_user_filter = FilteringStore.__dict__["get_user_filter"]
diff --git a/synapse/replication/slave/storage/groups.py b/synapse/replication/slave/storage/groups.py
index 28a46edd28..69a4ae42f9 100644
--- a/synapse/replication/slave/storage/groups.py
+++ b/synapse/replication/slave/storage/groups.py
@@ -14,6 +14,7 @@
 # limitations under the License.
 
 from synapse.storage import DataStore
+from synapse.storage.database import Database
 from synapse.util.caches.stream_change_cache import StreamChangeCache
 
 from ._base import BaseSlavedStore, __func__
@@ -21,8 +22,8 @@ from ._slaved_id_tracker import SlavedIdTracker
 
 
 class SlavedGroupServerStore(BaseSlavedStore):
-    def __init__(self, db_conn, hs):
-        super(SlavedGroupServerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SlavedGroupServerStore, self).__init__(database, db_conn, hs)
 
         self.hs = hs
 
diff --git a/synapse/replication/slave/storage/presence.py b/synapse/replication/slave/storage/presence.py
index 747ced0c84..f552e7c972 100644
--- a/synapse/replication/slave/storage/presence.py
+++ b/synapse/replication/slave/storage/presence.py
@@ -15,6 +15,7 @@
 
 from synapse.storage import DataStore
 from synapse.storage.data_stores.main.presence import PresenceStore
+from synapse.storage.database import Database
 from synapse.util.caches.stream_change_cache import StreamChangeCache
 
 from ._base import BaseSlavedStore, __func__
@@ -22,8 +23,8 @@ from ._slaved_id_tracker import SlavedIdTracker
 
 
 class SlavedPresenceStore(BaseSlavedStore):
-    def __init__(self, db_conn, hs):
-        super(SlavedPresenceStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SlavedPresenceStore, self).__init__(database, db_conn, hs)
         self._presence_id_gen = SlavedIdTracker(db_conn, "presence_stream", "stream_id")
 
         self._presence_on_startup = self._get_active_presence(db_conn)
diff --git a/synapse/replication/slave/storage/push_rule.py b/synapse/replication/slave/storage/push_rule.py
index 3655f05e54..eebd5a1fb6 100644
--- a/synapse/replication/slave/storage/push_rule.py
+++ b/synapse/replication/slave/storage/push_rule.py
@@ -15,17 +15,18 @@
 # limitations under the License.
 
 from synapse.storage.data_stores.main.push_rule import PushRulesWorkerStore
+from synapse.storage.database import Database
 
 from ._slaved_id_tracker import SlavedIdTracker
 from .events import SlavedEventStore
 
 
 class SlavedPushRuleStore(SlavedEventStore, PushRulesWorkerStore):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         self._push_rules_stream_id_gen = SlavedIdTracker(
             db_conn, "push_rules_stream", "stream_id"
         )
-        super(SlavedPushRuleStore, self).__init__(db_conn, hs)
+        super(SlavedPushRuleStore, self).__init__(database, db_conn, hs)
 
     def get_push_rules_stream_token(self):
         return (
diff --git a/synapse/replication/slave/storage/pushers.py b/synapse/replication/slave/storage/pushers.py
index b4331d0799..f22c2d44a3 100644
--- a/synapse/replication/slave/storage/pushers.py
+++ b/synapse/replication/slave/storage/pushers.py
@@ -15,14 +15,15 @@
 # limitations under the License.
 
 from synapse.storage.data_stores.main.pusher import PusherWorkerStore
+from synapse.storage.database import Database
 
 from ._base import BaseSlavedStore
 from ._slaved_id_tracker import SlavedIdTracker
 
 
 class SlavedPusherStore(PusherWorkerStore, BaseSlavedStore):
-    def __init__(self, db_conn, hs):
-        super(SlavedPusherStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SlavedPusherStore, self).__init__(database, db_conn, hs)
         self._pushers_id_gen = SlavedIdTracker(
             db_conn, "pushers", "id", extra_tables=[("deleted_pushers", "stream_id")]
         )
diff --git a/synapse/replication/slave/storage/receipts.py b/synapse/replication/slave/storage/receipts.py
index 43d823c601..d40dc6e1f5 100644
--- a/synapse/replication/slave/storage/receipts.py
+++ b/synapse/replication/slave/storage/receipts.py
@@ -15,6 +15,7 @@
 # limitations under the License.
 
 from synapse.storage.data_stores.main.receipts import ReceiptsWorkerStore
+from synapse.storage.database import Database
 
 from ._base import BaseSlavedStore
 from ._slaved_id_tracker import SlavedIdTracker
@@ -29,14 +30,14 @@ from ._slaved_id_tracker import SlavedIdTracker
 
 
 class SlavedReceiptsStore(ReceiptsWorkerStore, BaseSlavedStore):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         # We instantiate this first as the ReceiptsWorkerStore constructor
         # needs to be able to call get_max_receipt_stream_id
         self._receipts_id_gen = SlavedIdTracker(
             db_conn, "receipts_linearized", "stream_id"
         )
 
-        super(SlavedReceiptsStore, self).__init__(db_conn, hs)
+        super(SlavedReceiptsStore, self).__init__(database, db_conn, hs)
 
     def get_max_receipt_stream_id(self):
         return self._receipts_id_gen.get_current_token()
diff --git a/synapse/replication/slave/storage/room.py b/synapse/replication/slave/storage/room.py
index d9ad386b28..3a20f45316 100644
--- a/synapse/replication/slave/storage/room.py
+++ b/synapse/replication/slave/storage/room.py
@@ -14,14 +14,15 @@
 # limitations under the License.
 
 from synapse.storage.data_stores.main.room import RoomWorkerStore
+from synapse.storage.database import Database
 
 from ._base import BaseSlavedStore
 from ._slaved_id_tracker import SlavedIdTracker
 
 
 class RoomStore(RoomWorkerStore, BaseSlavedStore):
-    def __init__(self, db_conn, hs):
-        super(RoomStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RoomStore, self).__init__(database, db_conn, hs)
         self._public_room_id_gen = SlavedIdTracker(
             db_conn, "public_room_list_stream", "stream_id"
         )
diff --git a/synapse/server.py b/synapse/server.py
index be9af7f986..2db3dab221 100644
--- a/synapse/server.py
+++ b/synapse/server.py
@@ -238,8 +238,7 @@ class HomeServer(object):
     def setup(self):
         logger.info("Setting up.")
         with self.get_db_conn() as conn:
-            datastore = self.DATASTORE_CLASS(conn, self)
-            self.datastores = DataStores(datastore, conn, self)
+            self.datastores = DataStores(self.DATASTORE_CLASS, conn, self)
             conn.commit()
         self.start_time = int(self.get_clock().time())
         logger.info("Finished setting up.")
diff --git a/synapse/storage/__init__.py b/synapse/storage/__init__.py
index 8fb18203dc..ec89f645d4 100644
--- a/synapse/storage/__init__.py
+++ b/synapse/storage/__init__.py
@@ -49,15 +49,3 @@ class Storage(object):
         self.persistence = EventsPersistenceStorage(hs, stores)
         self.purge_events = PurgeEventsStorage(hs, stores)
         self.state = StateGroupStorage(hs, stores)
-
-
-def are_all_users_on_domain(txn, database_engine, domain):
-    sql = database_engine.convert_param_style(
-        "SELECT COUNT(*) FROM users WHERE name NOT LIKE ?"
-    )
-    pat = "%:" + domain
-    txn.execute(sql, (pat,))
-    num_not_matching = txn.fetchall()[0][0]
-    if num_not_matching == 0:
-        return True
-    return False
diff --git a/synapse/storage/_base.py b/synapse/storage/_base.py
index b7e27d4e97..b7637b5dc0 100644
--- a/synapse/storage/_base.py
+++ b/synapse/storage/_base.py
@@ -37,11 +37,11 @@ class SQLBaseStore(object):
     per data store (and not one per physical database).
     """
 
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         self.hs = hs
         self._clock = hs.get_clock()
         self.database_engine = hs.database_engine
-        self.db = Database(hs)  # In future this will be passed in
+        self.db = database
         self.rand = random.SystemRandom()
 
     def _invalidate_state_caches(self, room_id, members_changed):
diff --git a/synapse/storage/background_updates.py b/synapse/storage/background_updates.py
index a9a13a2658..4f97fd5ab6 100644
--- a/synapse/storage/background_updates.py
+++ b/synapse/storage/background_updates.py
@@ -379,7 +379,7 @@ class BackgroundUpdater(object):
             logger.debug("[SQL] %s", sql)
             c.execute(sql)
 
-        if isinstance(self.db.database_engine, engines.PostgresEngine):
+        if isinstance(self.db.engine, engines.PostgresEngine):
             runner = create_index_psql
         elif psql_only:
             runner = None
diff --git a/synapse/storage/data_stores/__init__.py b/synapse/storage/data_stores/__init__.py
index cb184a98cc..cafedd5c0d 100644
--- a/synapse/storage/data_stores/__init__.py
+++ b/synapse/storage/data_stores/__init__.py
@@ -13,6 +13,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from synapse.storage.database import Database
+from synapse.storage.prepare_database import prepare_database
+
 
 class DataStores(object):
     """The various data stores.
@@ -20,7 +23,14 @@ class DataStores(object):
     These are low level interfaces to physical databases.
     """
 
-    def __init__(self, main_store, db_conn, hs):
-        # Note we pass in the main store here as workers use a different main
+    def __init__(self, main_store_class, db_conn, hs):
+        # Note we pass in the main store class here as workers use a different main
         # store.
-        self.main = main_store
+        database = Database(hs)
+
+        # Check that db is correctly configured.
+        database.engine.check_database(db_conn.cursor())
+
+        prepare_database(db_conn, database.engine, config=hs.config)
+
+        self.main = main_store_class(database, db_conn, hs)
diff --git a/synapse/storage/data_stores/main/__init__.py b/synapse/storage/data_stores/main/__init__.py
index 6adb8adb04..c577c0df5f 100644
--- a/synapse/storage/data_stores/main/__init__.py
+++ b/synapse/storage/data_stores/main/__init__.py
@@ -20,6 +20,7 @@ import logging
 import time
 
 from synapse.api.constants import PresenceState
+from synapse.storage.database import Database
 from synapse.storage.engines import PostgresEngine
 from synapse.storage.util.id_generators import (
     ChainedIdGenerator,
@@ -111,10 +112,20 @@ class DataStore(
     RelationsStore,
     CacheInvalidationStore,
 ):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         self.hs = hs
         self._clock = hs.get_clock()
-        self.database_engine = hs.database_engine
+        self.database_engine = database.engine
+
+        all_users_native = are_all_users_on_domain(
+            db_conn.cursor(), database.engine, hs.hostname
+        )
+        if not all_users_native:
+            raise Exception(
+                "Found users in database not native to %s!\n"
+                "You cannot changed a synapse server_name after it's been configured"
+                % (hs.hostname,)
+            )
 
         self._stream_id_gen = StreamIdGenerator(
             db_conn,
@@ -169,7 +180,7 @@ class DataStore(
         else:
             self._cache_id_gen = None
 
-        super(DataStore, self).__init__(db_conn, hs)
+        super(DataStore, self).__init__(database, db_conn, hs)
 
         self._presence_on_startup = self._get_active_presence(db_conn)
 
@@ -554,3 +565,15 @@ class DataStore(
             retcols=["name", "password_hash", "is_guest", "admin", "user_type"],
             desc="search_users",
         )
+
+
+def are_all_users_on_domain(txn, database_engine, domain):
+    sql = database_engine.convert_param_style(
+        "SELECT COUNT(*) FROM users WHERE name NOT LIKE ?"
+    )
+    pat = "%:" + domain
+    txn.execute(sql, (pat,))
+    num_not_matching = txn.fetchall()[0][0]
+    if num_not_matching == 0:
+        return True
+    return False
diff --git a/synapse/storage/data_stores/main/account_data.py b/synapse/storage/data_stores/main/account_data.py
index 1a3dd7be8d..46b494b334 100644
--- a/synapse/storage/data_stores/main/account_data.py
+++ b/synapse/storage/data_stores/main/account_data.py
@@ -22,6 +22,7 @@ from canonicaljson import json
 from twisted.internet import defer
 
 from synapse.storage._base import SQLBaseStore
+from synapse.storage.database import Database
 from synapse.storage.util.id_generators import StreamIdGenerator
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks
 from synapse.util.caches.stream_change_cache import StreamChangeCache
@@ -38,13 +39,13 @@ class AccountDataWorkerStore(SQLBaseStore):
     # the abstract methods being implemented.
     __metaclass__ = abc.ABCMeta
 
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         account_max = self.get_max_account_data_stream_id()
         self._account_data_stream_cache = StreamChangeCache(
             "AccountDataAndTagsChangeCache", account_max
         )
 
-        super(AccountDataWorkerStore, self).__init__(db_conn, hs)
+        super(AccountDataWorkerStore, self).__init__(database, db_conn, hs)
 
     @abc.abstractmethod
     def get_max_account_data_stream_id(self):
@@ -270,12 +271,12 @@ class AccountDataWorkerStore(SQLBaseStore):
 
 
 class AccountDataStore(AccountDataWorkerStore):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         self._account_data_id_gen = StreamIdGenerator(
             db_conn, "account_data_max_stream_id", "stream_id"
         )
 
-        super(AccountDataStore, self).__init__(db_conn, hs)
+        super(AccountDataStore, self).__init__(database, db_conn, hs)
 
     def get_max_account_data_stream_id(self):
         """Get the current max stream id for the private user data stream
diff --git a/synapse/storage/data_stores/main/appservice.py b/synapse/storage/data_stores/main/appservice.py
index 6b2e12719c..b2f39649fd 100644
--- a/synapse/storage/data_stores/main/appservice.py
+++ b/synapse/storage/data_stores/main/appservice.py
@@ -24,6 +24,7 @@ from synapse.appservice import AppServiceTransaction
 from synapse.config.appservice import load_appservices
 from synapse.storage._base import SQLBaseStore
 from synapse.storage.data_stores.main.events_worker import EventsWorkerStore
+from synapse.storage.database import Database
 
 logger = logging.getLogger(__name__)
 
@@ -48,13 +49,13 @@ def _make_exclusive_regex(services_cache):
 
 
 class ApplicationServiceWorkerStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         self.services_cache = load_appservices(
             hs.hostname, hs.config.app_service_config_files
         )
         self.exclusive_user_regex = _make_exclusive_regex(self.services_cache)
 
-        super(ApplicationServiceWorkerStore, self).__init__(db_conn, hs)
+        super(ApplicationServiceWorkerStore, self).__init__(database, db_conn, hs)
 
     def get_app_services(self):
         return self.services_cache
diff --git a/synapse/storage/data_stores/main/client_ips.py b/synapse/storage/data_stores/main/client_ips.py
index 7b470a58f1..320c5b0f07 100644
--- a/synapse/storage/data_stores/main/client_ips.py
+++ b/synapse/storage/data_stores/main/client_ips.py
@@ -21,6 +21,7 @@ from twisted.internet import defer
 
 from synapse.metrics.background_process_metrics import wrap_as_background_process
 from synapse.storage._base import SQLBaseStore
+from synapse.storage.database import Database
 from synapse.util.caches import CACHE_SIZE_FACTOR
 from synapse.util.caches.descriptors import Cache
 
@@ -33,8 +34,8 @@ LAST_SEEN_GRANULARITY = 120 * 1000
 
 
 class ClientIpBackgroundUpdateStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(ClientIpBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(ClientIpBackgroundUpdateStore, self).__init__(database, db_conn, hs)
 
         self.db.updates.register_background_index_update(
             "user_ips_device_index",
@@ -363,13 +364,13 @@ class ClientIpBackgroundUpdateStore(SQLBaseStore):
 
 
 class ClientIpStore(ClientIpBackgroundUpdateStore):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
 
         self.client_ip_last_seen = Cache(
             name="client_ip_last_seen", keylen=4, max_entries=50000 * CACHE_SIZE_FACTOR
         )
 
-        super(ClientIpStore, self).__init__(db_conn, hs)
+        super(ClientIpStore, self).__init__(database, db_conn, hs)
 
         self.user_ips_max_age = hs.config.user_ips_max_age
 
diff --git a/synapse/storage/data_stores/main/deviceinbox.py b/synapse/storage/data_stores/main/deviceinbox.py
index 3c9f09301a..85cfa16850 100644
--- a/synapse/storage/data_stores/main/deviceinbox.py
+++ b/synapse/storage/data_stores/main/deviceinbox.py
@@ -21,6 +21,7 @@ from twisted.internet import defer
 
 from synapse.logging.opentracing import log_kv, set_tag, trace
 from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
+from synapse.storage.database import Database
 from synapse.util.caches.expiringcache import ExpiringCache
 
 logger = logging.getLogger(__name__)
@@ -210,8 +211,8 @@ class DeviceInboxWorkerStore(SQLBaseStore):
 class DeviceInboxBackgroundUpdateStore(SQLBaseStore):
     DEVICE_INBOX_STREAM_ID = "device_inbox_stream_drop"
 
-    def __init__(self, db_conn, hs):
-        super(DeviceInboxBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(DeviceInboxBackgroundUpdateStore, self).__init__(database, db_conn, hs)
 
         self.db.updates.register_background_index_update(
             "device_inbox_stream_index",
@@ -241,8 +242,8 @@ class DeviceInboxBackgroundUpdateStore(SQLBaseStore):
 class DeviceInboxStore(DeviceInboxWorkerStore, DeviceInboxBackgroundUpdateStore):
     DEVICE_INBOX_STREAM_ID = "device_inbox_stream_drop"
 
-    def __init__(self, db_conn, hs):
-        super(DeviceInboxStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(DeviceInboxStore, self).__init__(database, db_conn, hs)
 
         # Map of (user_id, device_id) to the last stream_id that has been
         # deleted up to. This is so that we can no op deletions.
diff --git a/synapse/storage/data_stores/main/devices.py b/synapse/storage/data_stores/main/devices.py
index 91ddaf137e..9a828231c4 100644
--- a/synapse/storage/data_stores/main/devices.py
+++ b/synapse/storage/data_stores/main/devices.py
@@ -31,6 +31,7 @@ from synapse.logging.opentracing import (
 )
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.storage._base import SQLBaseStore, db_to_json, make_in_list_sql_clause
+from synapse.storage.database import Database
 from synapse.types import get_verify_key_from_cross_signing_key
 from synapse.util import batch_iter
 from synapse.util.caches.descriptors import (
@@ -642,8 +643,8 @@ class DeviceWorkerStore(SQLBaseStore):
 
 
 class DeviceBackgroundUpdateStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(DeviceBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(DeviceBackgroundUpdateStore, self).__init__(database, db_conn, hs)
 
         self.db.updates.register_background_index_update(
             "device_lists_stream_idx",
@@ -692,8 +693,8 @@ class DeviceBackgroundUpdateStore(SQLBaseStore):
 
 
 class DeviceStore(DeviceWorkerStore, DeviceBackgroundUpdateStore):
-    def __init__(self, db_conn, hs):
-        super(DeviceStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(DeviceStore, self).__init__(database, db_conn, hs)
 
         # Map of (user_id, device_id) -> bool. If there is an entry that implies
         # the device exists.
diff --git a/synapse/storage/data_stores/main/event_federation.py b/synapse/storage/data_stores/main/event_federation.py
index 31d2e8eb28..1f517e8fad 100644
--- a/synapse/storage/data_stores/main/event_federation.py
+++ b/synapse/storage/data_stores/main/event_federation.py
@@ -28,6 +28,7 @@ from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
 from synapse.storage.data_stores.main.events_worker import EventsWorkerStore
 from synapse.storage.data_stores.main.signatures import SignatureWorkerStore
+from synapse.storage.database import Database
 from synapse.util.caches.descriptors import cached
 
 logger = logging.getLogger(__name__)
@@ -491,8 +492,8 @@ class EventFederationStore(EventFederationWorkerStore):
 
     EVENT_AUTH_STATE_ONLY = "event_auth_state_only"
 
-    def __init__(self, db_conn, hs):
-        super(EventFederationStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(EventFederationStore, self).__init__(database, db_conn, hs)
 
         self.db.updates.register_background_update_handler(
             self.EVENT_AUTH_STATE_ONLY, self._background_delete_non_state_event_auth
diff --git a/synapse/storage/data_stores/main/event_push_actions.py b/synapse/storage/data_stores/main/event_push_actions.py
index eec054cd48..9988a6d3fc 100644
--- a/synapse/storage/data_stores/main/event_push_actions.py
+++ b/synapse/storage/data_stores/main/event_push_actions.py
@@ -24,6 +24,7 @@ from twisted.internet import defer
 
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.storage._base import LoggingTransaction, SQLBaseStore
+from synapse.storage.database import Database
 from synapse.util.caches.descriptors import cachedInlineCallbacks
 
 logger = logging.getLogger(__name__)
@@ -68,8 +69,8 @@ def _deserialize_action(actions, is_highlight):
 
 
 class EventPushActionsWorkerStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(EventPushActionsWorkerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(EventPushActionsWorkerStore, self).__init__(database, db_conn, hs)
 
         # These get correctly set by _find_stream_orderings_for_times_txn
         self.stream_ordering_month_ago = None
@@ -611,8 +612,8 @@ class EventPushActionsWorkerStore(SQLBaseStore):
 class EventPushActionsStore(EventPushActionsWorkerStore):
     EPA_HIGHLIGHT_INDEX = "epa_highlight_index"
 
-    def __init__(self, db_conn, hs):
-        super(EventPushActionsStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(EventPushActionsStore, self).__init__(database, db_conn, hs)
 
         self.db.updates.register_background_index_update(
             self.EPA_HIGHLIGHT_INDEX,
diff --git a/synapse/storage/data_stores/main/events.py b/synapse/storage/data_stores/main/events.py
index d644c82784..da1529f6ea 100644
--- a/synapse/storage/data_stores/main/events.py
+++ b/synapse/storage/data_stores/main/events.py
@@ -41,6 +41,7 @@ from synapse.storage._base import make_in_list_sql_clause
 from synapse.storage.data_stores.main.event_federation import EventFederationStore
 from synapse.storage.data_stores.main.events_worker import EventsWorkerStore
 from synapse.storage.data_stores.main.state import StateGroupWorkerStore
+from synapse.storage.database import Database
 from synapse.types import RoomStreamToken, get_domain_from_id
 from synapse.util import batch_iter
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks
@@ -95,8 +96,8 @@ def _retry_on_integrity_error(func):
 class EventsStore(
     StateGroupWorkerStore, EventFederationStore, EventsWorkerStore,
 ):
-    def __init__(self, db_conn, hs):
-        super(EventsStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(EventsStore, self).__init__(database, db_conn, hs)
 
         # Collect metrics on the number of forward extremities that exist.
         # Counter of number of extremities to count
diff --git a/synapse/storage/data_stores/main/events_bg_updates.py b/synapse/storage/data_stores/main/events_bg_updates.py
index cb1fc30c31..efee17b929 100644
--- a/synapse/storage/data_stores/main/events_bg_updates.py
+++ b/synapse/storage/data_stores/main/events_bg_updates.py
@@ -23,6 +23,7 @@ from twisted.internet import defer
 
 from synapse.api.constants import EventContentFields
 from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
+from synapse.storage.database import Database
 
 logger = logging.getLogger(__name__)
 
@@ -33,8 +34,8 @@ class EventsBackgroundUpdatesStore(SQLBaseStore):
     EVENT_FIELDS_SENDER_URL_UPDATE_NAME = "event_fields_sender_url"
     DELETE_SOFT_FAILED_EXTREMITIES = "delete_soft_failed_extremities"
 
-    def __init__(self, db_conn, hs):
-        super(EventsBackgroundUpdatesStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(EventsBackgroundUpdatesStore, self).__init__(database, db_conn, hs)
 
         self.db.updates.register_background_update_handler(
             self.EVENT_ORIGIN_SERVER_TS_NAME, self._background_reindex_origin_server_ts
diff --git a/synapse/storage/data_stores/main/events_worker.py b/synapse/storage/data_stores/main/events_worker.py
index e041fc5eac..9ee117ce0f 100644
--- a/synapse/storage/data_stores/main/events_worker.py
+++ b/synapse/storage/data_stores/main/events_worker.py
@@ -33,6 +33,7 @@ from synapse.events.utils import prune_event
 from synapse.logging.context import LoggingContext, PreserveLoggingContext
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
+from synapse.storage.database import Database
 from synapse.types import get_domain_from_id
 from synapse.util import batch_iter
 from synapse.util.caches.descriptors import Cache
@@ -55,8 +56,8 @@ _EventCacheEntry = namedtuple("_EventCacheEntry", ("event", "redacted_event"))
 
 
 class EventsWorkerStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(EventsWorkerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(EventsWorkerStore, self).__init__(database, db_conn, hs)
 
         self._get_event_cache = Cache(
             "*getEvent*", keylen=3, max_entries=hs.config.event_cache_size
diff --git a/synapse/storage/data_stores/main/media_repository.py b/synapse/storage/data_stores/main/media_repository.py
index 03c9c6f8ae..80ca36dedf 100644
--- a/synapse/storage/data_stores/main/media_repository.py
+++ b/synapse/storage/data_stores/main/media_repository.py
@@ -13,11 +13,14 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 from synapse.storage._base import SQLBaseStore
+from synapse.storage.database import Database
 
 
 class MediaRepositoryBackgroundUpdateStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(MediaRepositoryBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(MediaRepositoryBackgroundUpdateStore, self).__init__(
+            database, db_conn, hs
+        )
 
         self.db.updates.register_background_index_update(
             update_name="local_media_repository_url_idx",
@@ -31,8 +34,8 @@ class MediaRepositoryBackgroundUpdateStore(SQLBaseStore):
 class MediaRepositoryStore(MediaRepositoryBackgroundUpdateStore):
     """Persistence for attachments and avatars"""
 
-    def __init__(self, db_conn, hs):
-        super(MediaRepositoryStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(MediaRepositoryStore, self).__init__(database, db_conn, hs)
 
     def get_local_media(self, media_id):
         """Get the metadata for a local piece of media
diff --git a/synapse/storage/data_stores/main/monthly_active_users.py b/synapse/storage/data_stores/main/monthly_active_users.py
index 34bf3a1880..27158534cb 100644
--- a/synapse/storage/data_stores/main/monthly_active_users.py
+++ b/synapse/storage/data_stores/main/monthly_active_users.py
@@ -17,6 +17,7 @@ import logging
 from twisted.internet import defer
 
 from synapse.storage._base import SQLBaseStore
+from synapse.storage.database import Database
 from synapse.util.caches.descriptors import cached
 
 logger = logging.getLogger(__name__)
@@ -27,13 +28,13 @@ LAST_SEEN_GRANULARITY = 60 * 60 * 1000
 
 
 class MonthlyActiveUsersStore(SQLBaseStore):
-    def __init__(self, dbconn, hs):
-        super(MonthlyActiveUsersStore, self).__init__(None, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(MonthlyActiveUsersStore, self).__init__(database, db_conn, hs)
         self._clock = hs.get_clock()
         self.hs = hs
         # Do not add more reserved users than the total allowable number
         self.db.new_transaction(
-            dbconn,
+            db_conn,
             "initialise_mau_threepids",
             [],
             [],
diff --git a/synapse/storage/data_stores/main/push_rule.py b/synapse/storage/data_stores/main/push_rule.py
index de682cc63a..5ba13aa973 100644
--- a/synapse/storage/data_stores/main/push_rule.py
+++ b/synapse/storage/data_stores/main/push_rule.py
@@ -27,6 +27,7 @@ from synapse.storage.data_stores.main.appservice import ApplicationServiceWorker
 from synapse.storage.data_stores.main.pusher import PusherWorkerStore
 from synapse.storage.data_stores.main.receipts import ReceiptsWorkerStore
 from synapse.storage.data_stores.main.roommember import RoomMemberWorkerStore
+from synapse.storage.database import Database
 from synapse.storage.push_rule import InconsistentRuleException, RuleNotFoundException
 from synapse.util.caches.descriptors import cachedInlineCallbacks, cachedList
 from synapse.util.caches.stream_change_cache import StreamChangeCache
@@ -72,8 +73,8 @@ class PushRulesWorkerStore(
     # the abstract methods being implemented.
     __metaclass__ = abc.ABCMeta
 
-    def __init__(self, db_conn, hs):
-        super(PushRulesWorkerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(PushRulesWorkerStore, self).__init__(database, db_conn, hs)
 
         push_rules_prefill, push_rules_id = self.db.get_cache_dict(
             db_conn,
diff --git a/synapse/storage/data_stores/main/receipts.py b/synapse/storage/data_stores/main/receipts.py
index ac2d45bd5c..96e54d145e 100644
--- a/synapse/storage/data_stores/main/receipts.py
+++ b/synapse/storage/data_stores/main/receipts.py
@@ -22,6 +22,7 @@ from canonicaljson import json
 from twisted.internet import defer
 
 from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
+from synapse.storage.database import Database
 from synapse.storage.util.id_generators import StreamIdGenerator
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks, cachedList
 from synapse.util.caches.stream_change_cache import StreamChangeCache
@@ -38,8 +39,8 @@ class ReceiptsWorkerStore(SQLBaseStore):
     # the abstract methods being implemented.
     __metaclass__ = abc.ABCMeta
 
-    def __init__(self, db_conn, hs):
-        super(ReceiptsWorkerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(ReceiptsWorkerStore, self).__init__(database, db_conn, hs)
 
         self._receipts_stream_cache = StreamChangeCache(
             "ReceiptsRoomChangeCache", self.get_max_receipt_stream_id()
@@ -315,14 +316,14 @@ class ReceiptsWorkerStore(SQLBaseStore):
 
 
 class ReceiptsStore(ReceiptsWorkerStore):
-    def __init__(self, db_conn, hs):
+    def __init__(self, database: Database, db_conn, hs):
         # We instantiate this first as the ReceiptsWorkerStore constructor
         # needs to be able to call get_max_receipt_stream_id
         self._receipts_id_gen = StreamIdGenerator(
             db_conn, "receipts_linearized", "stream_id"
         )
 
-        super(ReceiptsStore, self).__init__(db_conn, hs)
+        super(ReceiptsStore, self).__init__(database, db_conn, hs)
 
     def get_max_receipt_stream_id(self):
         return self._receipts_id_gen.get_current_token()
diff --git a/synapse/storage/data_stores/main/registration.py b/synapse/storage/data_stores/main/registration.py
index 1ef143c6d8..5e8ecac0ea 100644
--- a/synapse/storage/data_stores/main/registration.py
+++ b/synapse/storage/data_stores/main/registration.py
@@ -27,6 +27,7 @@ from synapse.api.constants import UserTypes
 from synapse.api.errors import Codes, StoreError, SynapseError, ThreepidValidationError
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.storage._base import SQLBaseStore
+from synapse.storage.database import Database
 from synapse.types import UserID
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks
 
@@ -36,8 +37,8 @@ logger = logging.getLogger(__name__)
 
 
 class RegistrationWorkerStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(RegistrationWorkerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RegistrationWorkerStore, self).__init__(database, db_conn, hs)
 
         self.config = hs.config
         self.clock = hs.get_clock()
@@ -794,8 +795,8 @@ class RegistrationWorkerStore(SQLBaseStore):
 
 
 class RegistrationBackgroundUpdateStore(RegistrationWorkerStore):
-    def __init__(self, db_conn, hs):
-        super(RegistrationBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RegistrationBackgroundUpdateStore, self).__init__(database, db_conn, hs)
 
         self.clock = hs.get_clock()
         self.config = hs.config
@@ -920,8 +921,8 @@ class RegistrationBackgroundUpdateStore(RegistrationWorkerStore):
 
 
 class RegistrationStore(RegistrationBackgroundUpdateStore):
-    def __init__(self, db_conn, hs):
-        super(RegistrationStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RegistrationStore, self).__init__(database, db_conn, hs)
 
         self._account_validity = hs.config.account_validity
 
diff --git a/synapse/storage/data_stores/main/room.py b/synapse/storage/data_stores/main/room.py
index da42dae243..0148be20d3 100644
--- a/synapse/storage/data_stores/main/room.py
+++ b/synapse/storage/data_stores/main/room.py
@@ -29,6 +29,7 @@ from synapse.api.constants import EventTypes
 from synapse.api.errors import StoreError
 from synapse.storage._base import SQLBaseStore
 from synapse.storage.data_stores.main.search import SearchStore
+from synapse.storage.database import Database
 from synapse.types import ThirdPartyInstanceID
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks
 
@@ -361,8 +362,8 @@ class RoomWorkerStore(SQLBaseStore):
 
 
 class RoomBackgroundUpdateStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(RoomBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RoomBackgroundUpdateStore, self).__init__(database, db_conn, hs)
 
         self.config = hs.config
 
@@ -440,8 +441,8 @@ class RoomBackgroundUpdateStore(SQLBaseStore):
 
 
 class RoomStore(RoomBackgroundUpdateStore, RoomWorkerStore, SearchStore):
-    def __init__(self, db_conn, hs):
-        super(RoomStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RoomStore, self).__init__(database, db_conn, hs)
 
         self.config = hs.config
 
diff --git a/synapse/storage/data_stores/main/roommember.py b/synapse/storage/data_stores/main/roommember.py
index 929f6b0d39..92e3b9c512 100644
--- a/synapse/storage/data_stores/main/roommember.py
+++ b/synapse/storage/data_stores/main/roommember.py
@@ -32,6 +32,7 @@ from synapse.storage._base import (
     make_in_list_sql_clause,
 )
 from synapse.storage.data_stores.main.events_worker import EventsWorkerStore
+from synapse.storage.database import Database
 from synapse.storage.engines import Sqlite3Engine
 from synapse.storage.roommember import (
     GetRoomsForUserWithStreamOrdering,
@@ -54,8 +55,8 @@ _CURRENT_STATE_MEMBERSHIP_UPDATE_NAME = "current_state_events_membership"
 
 
 class RoomMemberWorkerStore(EventsWorkerStore):
-    def __init__(self, db_conn, hs):
-        super(RoomMemberWorkerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RoomMemberWorkerStore, self).__init__(database, db_conn, hs)
 
         # Is the current_state_events.membership up to date? Or is the
         # background update still running?
@@ -835,8 +836,8 @@ class RoomMemberWorkerStore(EventsWorkerStore):
 
 
 class RoomMemberBackgroundUpdateStore(SQLBaseStore):
-    def __init__(self, db_conn, hs):
-        super(RoomMemberBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RoomMemberBackgroundUpdateStore, self).__init__(database, db_conn, hs)
         self.db.updates.register_background_update_handler(
             _MEMBERSHIP_PROFILE_UPDATE_NAME, self._background_add_membership_profile
         )
@@ -991,8 +992,8 @@ class RoomMemberBackgroundUpdateStore(SQLBaseStore):
 
 
 class RoomMemberStore(RoomMemberWorkerStore, RoomMemberBackgroundUpdateStore):
-    def __init__(self, db_conn, hs):
-        super(RoomMemberStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(RoomMemberStore, self).__init__(database, db_conn, hs)
 
     def _store_room_members_txn(self, txn, events, backfilled):
         """Store a room member in the database.
diff --git a/synapse/storage/data_stores/main/search.py b/synapse/storage/data_stores/main/search.py
index ffa1817e64..4eec2fae5e 100644
--- a/synapse/storage/data_stores/main/search.py
+++ b/synapse/storage/data_stores/main/search.py
@@ -25,6 +25,7 @@ from twisted.internet import defer
 
 from synapse.api.errors import SynapseError
 from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
+from synapse.storage.database import Database
 from synapse.storage.engines import PostgresEngine, Sqlite3Engine
 
 logger = logging.getLogger(__name__)
@@ -42,8 +43,8 @@ class SearchBackgroundUpdateStore(SQLBaseStore):
     EVENT_SEARCH_USE_GIST_POSTGRES_NAME = "event_search_postgres_gist"
     EVENT_SEARCH_USE_GIN_POSTGRES_NAME = "event_search_postgres_gin"
 
-    def __init__(self, db_conn, hs):
-        super(SearchBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SearchBackgroundUpdateStore, self).__init__(database, db_conn, hs)
 
         if not hs.config.enable_search:
             return
@@ -342,8 +343,8 @@ class SearchBackgroundUpdateStore(SQLBaseStore):
 
 
 class SearchStore(SearchBackgroundUpdateStore):
-    def __init__(self, db_conn, hs):
-        super(SearchStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(SearchStore, self).__init__(database, db_conn, hs)
 
     def store_event_search_txn(self, txn, event, key, value):
         """Add event to the search table
diff --git a/synapse/storage/data_stores/main/state.py b/synapse/storage/data_stores/main/state.py
index 7d5a9f8128..9ef7b48c74 100644
--- a/synapse/storage/data_stores/main/state.py
+++ b/synapse/storage/data_stores/main/state.py
@@ -28,6 +28,7 @@ from synapse.events import EventBase
 from synapse.events.snapshot import EventContext
 from synapse.storage._base import SQLBaseStore
 from synapse.storage.data_stores.main.events_worker import EventsWorkerStore
+from synapse.storage.database import Database
 from synapse.storage.engines import PostgresEngine
 from synapse.storage.state import StateFilter
 from synapse.util.caches import get_cache_factor_for, intern_string
@@ -213,8 +214,8 @@ class StateGroupWorkerStore(
     STATE_GROUP_INDEX_UPDATE_NAME = "state_group_state_type_index"
     CURRENT_STATE_INDEX_UPDATE_NAME = "current_state_members_idx"
 
-    def __init__(self, db_conn, hs):
-        super(StateGroupWorkerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(StateGroupWorkerStore, self).__init__(database, db_conn, hs)
 
         # Originally the state store used a single DictionaryCache to cache the
         # event IDs for the state types in a given state group to avoid hammering
@@ -1029,8 +1030,8 @@ class StateBackgroundUpdateStore(StateGroupBackgroundUpdateStore):
     CURRENT_STATE_INDEX_UPDATE_NAME = "current_state_members_idx"
     EVENT_STATE_GROUP_INDEX_UPDATE_NAME = "event_to_state_groups_sg_index"
 
-    def __init__(self, db_conn, hs):
-        super(StateBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(StateBackgroundUpdateStore, self).__init__(database, db_conn, hs)
         self.db.updates.register_background_update_handler(
             self.STATE_GROUP_DEDUPLICATION_UPDATE_NAME,
             self._background_deduplicate_state,
@@ -1245,8 +1246,8 @@ class StateStore(StateGroupWorkerStore, StateBackgroundUpdateStore):
       * `state_groups_state`: Maps state group to state events.
     """
 
-    def __init__(self, db_conn, hs):
-        super(StateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(StateStore, self).__init__(database, db_conn, hs)
 
     def _store_event_state_mappings_txn(
         self, txn, events_and_contexts: Iterable[Tuple[EventBase, EventContext]]
diff --git a/synapse/storage/data_stores/main/stats.py b/synapse/storage/data_stores/main/stats.py
index 40579bf965..7bc186e9a1 100644
--- a/synapse/storage/data_stores/main/stats.py
+++ b/synapse/storage/data_stores/main/stats.py
@@ -22,6 +22,7 @@ from twisted.internet.defer import DeferredLock
 
 from synapse.api.constants import EventTypes, Membership
 from synapse.storage.data_stores.main.state_deltas import StateDeltasStore
+from synapse.storage.database import Database
 from synapse.storage.engines import PostgresEngine
 from synapse.util.caches.descriptors import cached
 
@@ -58,8 +59,8 @@ TYPE_TO_ORIGIN_TABLE = {"room": ("rooms", "room_id"), "user": ("users", "name")}
 
 
 class StatsStore(StateDeltasStore):
-    def __init__(self, db_conn, hs):
-        super(StatsStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(StatsStore, self).__init__(database, db_conn, hs)
 
         self.server_name = hs.hostname
         self.clock = self.hs.get_clock()
diff --git a/synapse/storage/data_stores/main/stream.py b/synapse/storage/data_stores/main/stream.py
index 2ff8c57109..140da8dad6 100644
--- a/synapse/storage/data_stores/main/stream.py
+++ b/synapse/storage/data_stores/main/stream.py
@@ -47,6 +47,7 @@ from twisted.internet import defer
 from synapse.logging.context import make_deferred_yieldable, run_in_background
 from synapse.storage._base import SQLBaseStore
 from synapse.storage.data_stores.main.events_worker import EventsWorkerStore
+from synapse.storage.database import Database
 from synapse.storage.engines import PostgresEngine
 from synapse.types import RoomStreamToken
 from synapse.util.caches.stream_change_cache import StreamChangeCache
@@ -251,8 +252,8 @@ class StreamWorkerStore(EventsWorkerStore, SQLBaseStore):
 
     __metaclass__ = abc.ABCMeta
 
-    def __init__(self, db_conn, hs):
-        super(StreamWorkerStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(StreamWorkerStore, self).__init__(database, db_conn, hs)
 
         events_max = self.get_room_max_stream_ordering()
         event_cache_prefill, min_event_val = self.db.get_cache_dict(
diff --git a/synapse/storage/data_stores/main/transactions.py b/synapse/storage/data_stores/main/transactions.py
index c0d155a43c..5b07c2fbc0 100644
--- a/synapse/storage/data_stores/main/transactions.py
+++ b/synapse/storage/data_stores/main/transactions.py
@@ -24,6 +24,7 @@ from twisted.internet import defer
 
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.storage._base import SQLBaseStore, db_to_json
+from synapse.storage.database import Database
 from synapse.util.caches.expiringcache import ExpiringCache
 
 # py2 sqlite has buffer hardcoded as only binary type, so we must use it,
@@ -52,8 +53,8 @@ class TransactionStore(SQLBaseStore):
     """A collection of queries for handling PDUs.
     """
 
-    def __init__(self, db_conn, hs):
-        super(TransactionStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(TransactionStore, self).__init__(database, db_conn, hs)
 
         self._clock.looping_call(self._start_cleanup_transactions, 30 * 60 * 1000)
 
diff --git a/synapse/storage/data_stores/main/user_directory.py b/synapse/storage/data_stores/main/user_directory.py
index 62ffb34b29..90c180ec6d 100644
--- a/synapse/storage/data_stores/main/user_directory.py
+++ b/synapse/storage/data_stores/main/user_directory.py
@@ -21,6 +21,7 @@ from twisted.internet import defer
 from synapse.api.constants import EventTypes, JoinRules
 from synapse.storage.data_stores.main.state import StateFilter
 from synapse.storage.data_stores.main.state_deltas import StateDeltasStore
+from synapse.storage.database import Database
 from synapse.storage.engines import PostgresEngine, Sqlite3Engine
 from synapse.types import get_domain_from_id, get_localpart_from_id
 from synapse.util.caches.descriptors import cached
@@ -37,8 +38,8 @@ class UserDirectoryBackgroundUpdateStore(StateDeltasStore):
     # add_users_who_share_private_rooms?
     SHARE_PRIVATE_WORKING_SET = 500
 
-    def __init__(self, db_conn, hs):
-        super(UserDirectoryBackgroundUpdateStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(UserDirectoryBackgroundUpdateStore, self).__init__(database, db_conn, hs)
 
         self.server_name = hs.hostname
 
@@ -549,8 +550,8 @@ class UserDirectoryStore(UserDirectoryBackgroundUpdateStore):
     # add_users_who_share_private_rooms?
     SHARE_PRIVATE_WORKING_SET = 500
 
-    def __init__(self, db_conn, hs):
-        super(UserDirectoryStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(UserDirectoryStore, self).__init__(database, db_conn, hs)
 
     def remove_from_user_dir(self, user_id):
         def _remove_from_user_dir_txn(txn):
diff --git a/synapse/storage/database.py b/synapse/storage/database.py
index 6843b7e7f8..ec19ae1d9d 100644
--- a/synapse/storage/database.py
+++ b/synapse/storage/database.py
@@ -234,7 +234,7 @@ class Database(object):
         #   to watch it
         self._txn_perf_counters = PerformanceCounters()
 
-        self.database_engine = hs.database_engine
+        self.engine = hs.database_engine
 
         # A set of tables that are not safe to use native upserts in.
         self._unsafe_to_upsert_tables = set(UNIQUE_INDEX_BACKGROUND_UPDATES.keys())
@@ -242,10 +242,10 @@ class Database(object):
         # We add the user_directory_search table to the blacklist on SQLite
         # because the existing search table does not have an index, making it
         # unsafe to use native upserts.
-        if isinstance(self.database_engine, Sqlite3Engine):
+        if isinstance(self.engine, Sqlite3Engine):
             self._unsafe_to_upsert_tables.add("user_directory_search")
 
-        if self.database_engine.can_native_upsert:
+        if self.engine.can_native_upsert:
             # Check ASAP (and then later, every 1s) to see if we have finished
             # background updates of tables that aren't safe to update.
             self._clock.call_later(
@@ -331,7 +331,7 @@ class Database(object):
                 cursor = LoggingTransaction(
                     conn.cursor(),
                     name,
-                    self.database_engine,
+                    self.engine,
                     after_callbacks,
                     exception_callbacks,
                 )
@@ -339,7 +339,7 @@ class Database(object):
                     r = func(cursor, *args, **kwargs)
                     conn.commit()
                     return r
-                except self.database_engine.module.OperationalError as e:
+                except self.engine.module.OperationalError as e:
                     # This can happen if the database disappears mid
                     # transaction.
                     logger.warning(
@@ -353,20 +353,20 @@ class Database(object):
                         i += 1
                         try:
                             conn.rollback()
-                        except self.database_engine.module.Error as e1:
+                        except self.engine.module.Error as e1:
                             logger.warning(
                                 "[TXN EROLL] {%s} %s", name, exception_to_unicode(e1)
                             )
                         continue
                     raise
-                except self.database_engine.module.DatabaseError as e:
-                    if self.database_engine.is_deadlock(e):
+                except self.engine.module.DatabaseError as e:
+                    if self.engine.is_deadlock(e):
                         logger.warning("[TXN DEADLOCK] {%s} %d/%d", name, i, N)
                         if i < N:
                             i += 1
                             try:
                                 conn.rollback()
-                            except self.database_engine.module.Error as e1:
+                            except self.engine.module.Error as e1:
                                 logger.warning(
                                     "[TXN EROLL] {%s} %s",
                                     name,
@@ -494,7 +494,7 @@ class Database(object):
                 sql_scheduling_timer.observe(sched_duration_sec)
                 context.add_database_scheduled(sched_duration_sec)
 
-                if self.database_engine.is_connection_closed(conn):
+                if self.engine.is_connection_closed(conn):
                     logger.debug("Reconnecting closed database connection")
                     conn.reconnect()
 
@@ -561,7 +561,7 @@ class Database(object):
         """
         try:
             yield self.runInteraction(desc, self.simple_insert_txn, table, values)
-        except self.database_engine.module.IntegrityError:
+        except self.engine.module.IntegrityError:
             # We have to do or_ignore flag at this layer, since we can't reuse
             # a cursor after we receive an error from the db.
             if not or_ignore:
@@ -660,7 +660,7 @@ class Database(object):
                     lock=lock,
                 )
                 return result
-            except self.database_engine.module.IntegrityError as e:
+            except self.engine.module.IntegrityError as e:
                 attempts += 1
                 if attempts >= 5:
                     # don't retry forever, because things other than races
@@ -692,10 +692,7 @@ class Database(object):
             upserts return True if a new entry was created, False if an existing
             one was updated.
         """
-        if (
-            self.database_engine.can_native_upsert
-            and table not in self._unsafe_to_upsert_tables
-        ):
+        if self.engine.can_native_upsert and table not in self._unsafe_to_upsert_tables:
             return self.simple_upsert_txn_native_upsert(
                 txn, table, keyvalues, values, insertion_values=insertion_values
             )
@@ -726,7 +723,7 @@ class Database(object):
         """
         # We need to lock the table :(, unless we're *really* careful
         if lock:
-            self.database_engine.lock_table(txn, table)
+            self.engine.lock_table(txn, table)
 
         def _getwhere(key):
             # If the value we're passing in is None (aka NULL), we need to use
@@ -828,10 +825,7 @@ class Database(object):
         Returns:
             None
         """
-        if (
-            self.database_engine.can_native_upsert
-            and table not in self._unsafe_to_upsert_tables
-        ):
+        if self.engine.can_native_upsert and table not in self._unsafe_to_upsert_tables:
             return self.simple_upsert_many_txn_native_upsert(
                 txn, table, key_names, key_values, value_names, value_values
             )
@@ -1301,7 +1295,7 @@ class Database(object):
             "limit": limit,
         }
 
-        sql = self.database_engine.convert_param_style(sql)
+        sql = self.engine.convert_param_style(sql)
 
         txn = db_conn.cursor()
         txn.execute(sql, (int(max_value),))
diff --git a/tests/replication/slave/storage/_base.py b/tests/replication/slave/storage/_base.py
index e7472e3a93..3dae83c543 100644
--- a/tests/replication/slave/storage/_base.py
+++ b/tests/replication/slave/storage/_base.py
@@ -20,6 +20,7 @@ from synapse.replication.tcp.client import (
     ReplicationClientHandler,
 )
 from synapse.replication.tcp.resource import ReplicationStreamProtocolFactory
+from synapse.storage.database import Database
 
 from tests import unittest
 from tests.server import FakeTransport
@@ -42,7 +43,9 @@ class BaseSlavedStoreTestCase(unittest.HomeserverTestCase):
 
         self.master_store = self.hs.get_datastore()
         self.storage = hs.get_storage()
-        self.slaved_store = self.STORE_TYPE(self.hs.get_db_conn(), self.hs)
+        self.slaved_store = self.STORE_TYPE(
+            Database(hs), self.hs.get_db_conn(), self.hs
+        )
         self.event_id = 0
 
         server_factory = ReplicationStreamProtocolFactory(self.hs)
diff --git a/tests/storage/test_appservice.py b/tests/storage/test_appservice.py
index dfeea24599..2e521e9ab7 100644
--- a/tests/storage/test_appservice.py
+++ b/tests/storage/test_appservice.py
@@ -28,6 +28,7 @@ from synapse.storage.data_stores.main.appservice import (
     ApplicationServiceStore,
     ApplicationServiceTransactionStore,
 )
+from synapse.storage.database import Database
 
 from tests import unittest
 from tests.utils import setup_test_homeserver
@@ -54,7 +55,8 @@ class ApplicationServiceStoreTestCase(unittest.TestCase):
         self._add_appservice("token2", "as2", "some_url", "some_hs_token", "bob")
         self._add_appservice("token3", "as3", "some_url", "some_hs_token", "bob")
         # must be done after inserts
-        self.store = ApplicationServiceStore(hs.get_db_conn(), hs)
+        database = Database(hs)
+        self.store = ApplicationServiceStore(database, hs.get_db_conn(), hs)
 
     def tearDown(self):
         # TODO: suboptimal that we need to create files for tests!
@@ -123,7 +125,8 @@ class ApplicationServiceTransactionStoreTestCase(unittest.TestCase):
 
         self.as_yaml_files = []
 
-        self.store = TestTransactionStore(hs.get_db_conn(), hs)
+        database = Database(hs)
+        self.store = TestTransactionStore(database, hs.get_db_conn(), hs)
 
     def _add_service(self, url, as_token, id):
         as_yaml = dict(
@@ -382,8 +385,8 @@ class ApplicationServiceTransactionStoreTestCase(unittest.TestCase):
 
 # required for ApplicationServiceTransactionStoreTestCase tests
 class TestTransactionStore(ApplicationServiceTransactionStore, ApplicationServiceStore):
-    def __init__(self, db_conn, hs):
-        super(TestTransactionStore, self).__init__(db_conn, hs)
+    def __init__(self, database: Database, db_conn, hs):
+        super(TestTransactionStore, self).__init__(database, db_conn, hs)
 
 
 class ApplicationServiceStoreConfigTestCase(unittest.TestCase):
@@ -416,7 +419,7 @@ class ApplicationServiceStoreConfigTestCase(unittest.TestCase):
         hs.config.event_cache_size = 1
         hs.config.password_providers = []
 
-        ApplicationServiceStore(hs.get_db_conn(), hs)
+        ApplicationServiceStore(Database(hs), hs.get_db_conn(), hs)
 
     @defer.inlineCallbacks
     def test_duplicate_ids(self):
@@ -432,7 +435,7 @@ class ApplicationServiceStoreConfigTestCase(unittest.TestCase):
         hs.config.password_providers = []
 
         with self.assertRaises(ConfigError) as cm:
-            ApplicationServiceStore(hs.get_db_conn(), hs)
+            ApplicationServiceStore(Database(hs), hs.get_db_conn(), hs)
 
         e = cm.exception
         self.assertIn(f1, str(e))
@@ -453,7 +456,7 @@ class ApplicationServiceStoreConfigTestCase(unittest.TestCase):
         hs.config.password_providers = []
 
         with self.assertRaises(ConfigError) as cm:
-            ApplicationServiceStore(hs.get_db_conn(), hs)
+            ApplicationServiceStore(Database(hs), hs.get_db_conn(), hs)
 
         e = cm.exception
         self.assertIn(f1, str(e))
diff --git a/tests/storage/test_base.py b/tests/storage/test_base.py
index 7915d48a9e..537cfe9f64 100644
--- a/tests/storage/test_base.py
+++ b/tests/storage/test_base.py
@@ -21,6 +21,7 @@ from mock import Mock
 from twisted.internet import defer
 
 from synapse.storage._base import SQLBaseStore
+from synapse.storage.database import Database
 from synapse.storage.engines import create_engine
 
 from tests import unittest
@@ -59,7 +60,7 @@ class SQLBaseStoreTestCase(unittest.TestCase):
             "test", db_pool=self.db_pool, config=config, database_engine=fake_engine
         )
 
-        self.datastore = SQLBaseStore(None, hs)
+        self.datastore = SQLBaseStore(Database(hs), None, hs)
 
     @defer.inlineCallbacks
     def test_insert_1col(self):
diff --git a/tests/storage/test_profile.py b/tests/storage/test_profile.py
index 24c7fe16c3..9b6f7211ae 100644
--- a/tests/storage/test_profile.py
+++ b/tests/storage/test_profile.py
@@ -16,7 +16,6 @@
 
 from twisted.internet import defer
 
-from synapse.storage.data_stores.main.profile import ProfileStore
 from synapse.types import UserID
 
 from tests import unittest
@@ -28,7 +27,7 @@ class ProfileStoreTestCase(unittest.TestCase):
     def setUp(self):
         hs = yield setup_test_homeserver(self.addCleanup)
 
-        self.store = ProfileStore(hs.get_db_conn(), hs)
+        self.store = hs.get_datastore()
 
         self.u_frank = UserID.from_string("@frank:test")
 
diff --git a/tests/storage/test_user_directory.py b/tests/storage/test_user_directory.py
index 7eea57c0e2..6a545d2eb0 100644
--- a/tests/storage/test_user_directory.py
+++ b/tests/storage/test_user_directory.py
@@ -15,8 +15,6 @@
 
 from twisted.internet import defer
 
-from synapse.storage.data_stores.main.user_directory import UserDirectoryStore
-
 from tests import unittest
 from tests.utils import setup_test_homeserver
 
@@ -29,7 +27,7 @@ class UserDirectoryStoreTestCase(unittest.TestCase):
     @defer.inlineCallbacks
     def setUp(self):
         self.hs = yield setup_test_homeserver(self.addCleanup)
-        self.store = UserDirectoryStore(self.hs.get_db_conn(), self.hs)
+        self.store = self.hs.get_datastore()
 
         # alice and bob are both in !room_id. bobby is not but shares
         # a homeserver with alice.
diff --git a/tests/test_federation.py b/tests/test_federation.py
index 7d82b58466..ad165d7295 100644
--- a/tests/test_federation.py
+++ b/tests/test_federation.py
@@ -33,6 +33,8 @@ class MessageAcceptTests(unittest.TestCase):
         self.reactor.advance(0.1)
         self.room_id = self.successResultOf(room)["room_id"]
 
+        self.store = self.homeserver.get_datastore()
+
         # Figure out what the most recent event is
         most_recent = self.successResultOf(
             maybeDeferred(
@@ -77,10 +79,7 @@ class MessageAcceptTests(unittest.TestCase):
         # Make sure we actually joined the room
         self.assertEqual(
             self.successResultOf(
-                maybeDeferred(
-                    self.homeserver.get_datastore().get_latest_event_ids_in_room,
-                    self.room_id,
-                )
+                maybeDeferred(self.store.get_latest_event_ids_in_room, self.room_id)
             )[0],
             "$join:test.serv",
         )
@@ -100,10 +99,7 @@ class MessageAcceptTests(unittest.TestCase):
 
         # Figure out what the most recent event is
         most_recent = self.successResultOf(
-            maybeDeferred(
-                self.homeserver.get_datastore().get_latest_event_ids_in_room,
-                self.room_id,
-            )
+            maybeDeferred(self.store.get_latest_event_ids_in_room, self.room_id)
         )[0]
 
         # Now lie about an event
@@ -141,7 +137,5 @@ class MessageAcceptTests(unittest.TestCase):
         )
 
         # Make sure the invalid event isn't there
-        extrem = maybeDeferred(
-            self.homeserver.get_datastore().get_latest_event_ids_in_room, self.room_id
-        )
+        extrem = maybeDeferred(self.store.get_latest_event_ids_in_room, self.room_id)
         self.assertEqual(self.successResultOf(extrem)[0], "$join:test.serv")