diff --git a/.buildkite/scripts/create_postgres_db.py b/.buildkite/scripts/create_postgres_db.py
index df6082b0ac..956339de5c 100755
--- a/.buildkite/scripts/create_postgres_db.py
+++ b/.buildkite/scripts/create_postgres_db.py
@@ -15,6 +15,7 @@
 # limitations under the License.
 
 import logging
+
 from synapse.storage.engines import create_engine
 
 logger = logging.getLogger("create_postgres_db")
diff --git a/changelog.d/9038.misc b/changelog.d/9038.misc
new file mode 100644
index 0000000000..5b9e21a1db
--- /dev/null
+++ b/changelog.d/9038.misc
@@ -0,0 +1 @@
+Configure the linters to run on a consistent set of files.
diff --git a/stubs/frozendict.pyi b/stubs/frozendict.pyi
index 3f3af59f26..0368ba4703 100644
--- a/stubs/frozendict.pyi
+++ b/stubs/frozendict.pyi
@@ -15,16 +15,7 @@
 
 # Stub for frozendict.
 
-from typing import (
-    Any,
-    Hashable,
-    Iterable,
-    Iterator,
-    Mapping,
-    overload,
-    Tuple,
-    TypeVar,
-)
+from typing import Any, Hashable, Iterable, Iterator, Mapping, Tuple, TypeVar, overload
 
 _KT = TypeVar("_KT", bound=Hashable)  # Key type.
 _VT = TypeVar("_VT")  # Value type.
diff --git a/stubs/sortedcontainers/sorteddict.pyi b/stubs/sortedcontainers/sorteddict.pyi
index 68779f968e..7b9fd079d9 100644
--- a/stubs/sortedcontainers/sorteddict.pyi
+++ b/stubs/sortedcontainers/sorteddict.pyi
@@ -7,17 +7,17 @@ from typing import (
     Callable,
     Dict,
     Hashable,
-    Iterator,
-    Iterable,
     ItemsView,
+    Iterable,
+    Iterator,
     KeysView,
     List,
     Mapping,
     Optional,
     Sequence,
+    Tuple,
     Type,
     TypeVar,
-    Tuple,
     Union,
     ValuesView,
     overload,
diff --git a/stubs/txredisapi.pyi b/stubs/txredisapi.pyi
index 522244bb57..bfac6840e6 100644
--- a/stubs/txredisapi.pyi
+++ b/stubs/txredisapi.pyi
@@ -16,7 +16,7 @@
 """Contains *incomplete* type hints for txredisapi.
 """
 
-from typing import List, Optional, Union, Type
+from typing import List, Optional, Type, Union
 
 class RedisProtocol:
     def publish(self, channel: str, message: bytes): ...
diff --git a/tox.ini b/tox.ini
index ab4ae295a9..297136fcc5 100644
--- a/tox.ini
+++ b/tox.ini
@@ -24,6 +24,20 @@ deps =
     # install the "enum34" dependency of cryptography.
     pip>=10
 
+# directories/files we run the linters on
+lint_targets =
+    setup.py
+    synapse
+    tests
+    scripts
+    scripts-dev
+    stubs
+    contrib
+    synctl
+    synmark
+    .buildkite
+    docker
+
 # default settings for all tox environments
 [testenv]
 deps =
@@ -130,13 +144,13 @@ commands =
 [testenv:check_codestyle]
 extras = lint
 commands =
-    python -m black --check --diff .
-    /bin/sh -c "flake8 synapse tests scripts scripts-dev contrib synctl {env:PEP8SUFFIX:}"
+    python -m black --check --diff {[base]lint_targets}
+    flake8 {[base]lint_targets} {env:PEP8SUFFIX:}
     {toxinidir}/scripts-dev/config-lint.sh
 
 [testenv:check_isort]
 extras = lint
-commands = /bin/sh -c "isort -c --df --sp setup.cfg synapse tests scripts-dev scripts"
+commands = isort -c --df --sp setup.cfg {[base]lint_targets}
 
 [testenv:check-newsfragment]
 skip_install = True