diff --git a/synapse/storage/devices.py b/synapse/storage/devices.py
index bc3f575b1e..ecdab34e7d 100644
--- a/synapse/storage/devices.py
+++ b/synapse/storage/devices.py
@@ -22,14 +22,19 @@ from twisted.internet import defer
 
 from synapse.api.errors import StoreError
 from synapse.metrics.background_process_metrics import run_as_background_process
+from synapse.storage.background_updates import BackgroundUpdateStore
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks, cachedList
 
-from ._base import Cache, SQLBaseStore, db_to_json
+from ._base import Cache, db_to_json
 
 logger = logging.getLogger(__name__)
 
+DROP_DEVICE_LIST_STREAMS_NON_UNIQUE_INDEXES = (
+    "drop_device_list_streams_non_unique_indexes"
+)
 
-class DeviceStore(SQLBaseStore):
+
+class DeviceStore(BackgroundUpdateStore):
     def __init__(self, db_conn, hs):
         super(DeviceStore, self).__init__(db_conn, hs)
 
@@ -52,6 +57,30 @@ class DeviceStore(SQLBaseStore):
             columns=["user_id", "device_id"],
         )
 
+        # create a unique index on device_lists_remote_cache
+        self.register_background_index_update(
+            "device_lists_remote_cache_unique_idx",
+            index_name="device_lists_remote_cache_unique_id",
+            table="device_lists_remote_cache",
+            columns=["user_id", "device_id"],
+            unique=True,
+        )
+
+        # And one on device_lists_remote_extremeties
+        self.register_background_index_update(
+            "device_lists_remote_extremeties_unique_idx",
+            index_name="device_lists_remote_extremeties_unique_idx",
+            table="device_lists_remote_extremeties",
+            columns=["user_id"],
+            unique=True,
+        )
+
+        # once they complete, we can remove the old non-unique indexes.
+        self.register_background_update_handler(
+            DROP_DEVICE_LIST_STREAMS_NON_UNIQUE_INDEXES,
+            self._drop_device_list_streams_non_unique_indexes,
+        )
+
     @defer.inlineCallbacks
     def store_device(self, user_id, device_id,
                      initial_device_display_name):
@@ -757,3 +786,19 @@ class DeviceStore(SQLBaseStore):
             "_prune_old_outbound_device_pokes",
             _prune_txn,
         )
+
+    @defer.inlineCallbacks
+    def _drop_device_list_streams_non_unique_indexes(self, progress, batch_size):
+        def f(conn):
+            txn = conn.cursor()
+            txn.execute(
+                "DROP INDEX IF EXISTS device_lists_remote_cache_id"
+            )
+            txn.execute(
+                "DROP INDEX IF EXISTS device_lists_remote_extremeties_id"
+            )
+            txn.close()
+
+        yield self.runWithConnection(f)
+        yield self._end_background_update(DROP_DEVICE_LIST_STREAMS_NON_UNIQUE_INDEXES)
+        defer.returnValue(1)
diff --git a/synapse/storage/schema/delta/40/device_list_streams.sql b/synapse/storage/schema/delta/40/device_list_streams.sql
index 54841b3843..dd6dcb65f1 100644
--- a/synapse/storage/schema/delta/40/device_list_streams.sql
+++ b/synapse/storage/schema/delta/40/device_list_streams.sql
@@ -20,9 +20,6 @@ CREATE TABLE device_lists_remote_cache (
     content TEXT NOT NULL
 );
 
-CREATE INDEX device_lists_remote_cache_id ON device_lists_remote_cache(user_id, device_id);
-
-
 -- The last update we got for a user. Empty if we're not receiving updates for
 -- that user.
 CREATE TABLE device_lists_remote_extremeties (
@@ -30,7 +27,11 @@ CREATE TABLE device_lists_remote_extremeties (
     stream_id TEXT NOT NULL
 );
 
-CREATE INDEX device_lists_remote_extremeties_id ON device_lists_remote_extremeties(user_id, stream_id);
+-- we used to create non-unique indexes on these tables, but as of update 52 we create
+-- unique indexes concurrently:
+--
+-- CREATE INDEX device_lists_remote_cache_id ON device_lists_remote_cache(user_id, device_id);
+-- CREATE INDEX device_lists_remote_extremeties_id ON device_lists_remote_extremeties(user_id, stream_id);
 
 
 -- Stream of device lists updates. Includes both local and remotes
diff --git a/synapse/storage/schema/delta/52/device_list_streams_unique_idx.sql b/synapse/storage/schema/delta/52/device_list_streams_unique_idx.sql
new file mode 100644
index 0000000000..bfa49e6f92
--- /dev/null
+++ b/synapse/storage/schema/delta/52/device_list_streams_unique_idx.sql
@@ -0,0 +1,36 @@
+/* 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.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+-- register a background update which will create a unique index on
+-- device_lists_remote_cache
+INSERT into background_updates (update_name, progress_json)
+    VALUES ('device_lists_remote_cache_unique_idx', '{}');
+
+-- and one on device_lists_remote_extremeties
+INSERT into background_updates (update_name, progress_json, depends_on)
+    VALUES (
+        'device_lists_remote_extremeties_unique_idx', '{}',
+
+        -- doesn't really depend on this, but we need to make sure both happen
+        -- before we drop the old indexes.
+        'device_lists_remote_cache_unique_idx'
+    );
+
+-- once they complete, we can drop the old indexes.
+INSERT into background_updates (update_name, progress_json, depends_on)
+    VALUES (
+        'drop_device_list_streams_non_unique_indexes', '{}',
+        'device_lists_remote_extremeties_unique_idx'
+    );