diff --git a/synapse/handlers/deactivate_account.py b/synapse/handlers/deactivate_account.py
index d58ea6c650..0277f80b75 100644
--- a/synapse/handlers/deactivate_account.py
+++ b/synapse/handlers/deactivate_account.py
@@ -17,6 +17,7 @@ from twisted.internet import defer, reactor
 from ._base import BaseHandler
 from synapse.types import UserID, create_requester
 from synapse.util.logcontext import run_in_background
+from synapse.api.errors import SynapseError
 
 import logging
 
@@ -30,6 +31,7 @@ class DeactivateAccountHandler(BaseHandler):
         self._auth_handler = hs.get_auth_handler()
         self._device_handler = hs.get_device_handler()
         self._room_member_handler = hs.get_room_member_handler()
+        self._identity_handler = hs.get_handlers().identity_handler
 
         # Flag that indicates whether the process to part users from rooms is running
         self._user_parter_running = False
@@ -51,6 +53,25 @@ class DeactivateAccountHandler(BaseHandler):
         # FIXME: Theoretically there is a race here wherein user resets
         # password using threepid.
 
+        # delete threepids first. We remove these from the IS so if this fails,
+        # leave the user still active so they can try again.
+        # Ideally we would prevent password resets and then do this in the
+        # background thread.
+        threepids = yield self.store.user_get_threepids(user_id)
+        for threepid in threepids:
+            try:
+                yield self._identity_handler.unbind_threepid(user_id,
+                    {
+                        'medium': threepid['medium'],
+                        'address': threepid['address'],
+                    },
+                )
+            except:
+                # Do we want this to be a fatal error or should we carry on?
+                logger.exception("Failed to remove threepid from ID server")
+                raise SynapseError(400, "Failed to remove threepid from ID server")
+            yield self.store.user_delete_threepid(user_id, threepid['medium'], threepid['address'])
+
         # first delete any devices belonging to the user, which will also
         # delete corresponding access tokens.
         yield self._device_handler.delete_all_devices_for_user(user_id)
@@ -58,7 +79,6 @@ class DeactivateAccountHandler(BaseHandler):
         # a device.
         yield self._auth_handler.delete_access_tokens_for_user(user_id)
 
-        yield self.store.user_delete_threepids(user_id)
         yield self.store.user_set_password_hash(user_id, None)
 
         # Add the user to a table of users pending deactivation (ie.
diff --git a/synapse/handlers/identity.py b/synapse/handlers/identity.py
index 91a0898860..67a89a1d72 100644
--- a/synapse/handlers/identity.py
+++ b/synapse/handlers/identity.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 # Copyright 2015, 2016 OpenMarket Ltd
 # Copyright 2017 Vector Creations Ltd
+# Copyright 2018 New Vector Ltd
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -38,6 +39,7 @@ class IdentityHandler(BaseHandler):
         super(IdentityHandler, self).__init__(hs)
 
         self.http_client = hs.get_simple_http_client()
+        self.federation_http_client = hs.get_http_client()
 
         self.trusted_id_servers = set(hs.config.trusted_third_party_id_servers)
         self.trust_any_id_server_just_for_testing_do_not_use = (
@@ -138,6 +140,39 @@ class IdentityHandler(BaseHandler):
             data = json.loads(e.msg)
         defer.returnValue(data)
 
+    @defer.inlineCallbacks
+    def unbind_threepid(self, mxid, threepid):
+        yield run_on_reactor()
+        logger.debug("unbinding threepid %r from %s", threepid, mxid)
+        if not self.trusted_id_servers:
+            logger.warn("Can't unbind threepid: no trusted ID servers set in config")
+            defer.returnValue(False)
+        id_server = next(iter(self.trusted_id_servers))
+
+        url = "https://%s/_matrix/identity/api/v1/3pid/unbind" % (id_server,)
+        content = {
+            "mxid": mxid,
+            "threepid": threepid,
+        }
+        headers = {}
+        # we abuse the federation http client to sign the request, but we have to send it
+        # using the normal http client since we don't want the SRV lookup and want normal
+        # 'browser-like' HTTPS.
+        self.federation_http_client.sign_request(
+            destination=None,
+            method='POST',
+            url_bytes='/_matrix/identity/api/v1/3pid/unbind'.encode('ascii'),
+            headers_dict=headers,
+            content=content,
+            destination_is=id_server,
+        )
+        yield self.http_client.post_json_get_json(
+            url,
+            content,
+            headers,
+        )
+        defer.returnValue(True)
+
     @defer.inlineCallbacks
     def requestEmailToken(self, id_server, email, client_secret, send_attempt, **kwargs):
         yield run_on_reactor()
diff --git a/synapse/http/matrixfederationclient.py b/synapse/http/matrixfederationclient.py
index 4b2b85464d..21eaf77dc4 100644
--- a/synapse/http/matrixfederationclient.py
+++ b/synapse/http/matrixfederationclient.py
@@ -262,14 +262,19 @@ class MatrixFederationHttpClient(object):
             defer.returnValue(response)
 
     def sign_request(self, destination, method, url_bytes, headers_dict,
-                     content=None):
+                     content=None, destination_is=None):
         request = {
             "method": method,
             "uri": url_bytes,
             "origin": self.server_name,
-            "destination": destination,
         }
 
+        if destination is not None:
+            request["destination"] = destination
+
+        if destination_is is not None:
+            request["destination_is"] = destination_is
+
         if content is not None:
             request["content"] = content
 
diff --git a/synapse/storage/registration.py b/synapse/storage/registration.py
index a530e29f43..5d8a850ac9 100644
--- a/synapse/storage/registration.py
+++ b/synapse/storage/registration.py
@@ -452,15 +452,6 @@ class RegistrationStore(RegistrationWorkerStore,
             defer.returnValue(ret['user_id'])
         defer.returnValue(None)
 
-    def user_delete_threepids(self, user_id):
-        return self._simple_delete(
-            "user_threepids",
-            keyvalues={
-                "user_id": user_id,
-            },
-            desc="user_delete_threepids",
-        )
-
     def user_delete_threepid(self, user_id, medium, address):
         return self._simple_delete(
             "user_threepids",