diff --git a/synapse/storage/deviceinbox.py b/synapse/storage/deviceinbox.py
index 2821eb89c9..b71ac3ae39 100644
--- a/synapse/storage/deviceinbox.py
+++ b/synapse/storage/deviceinbox.py
@@ -18,13 +18,29 @@ import ujson
 
 from twisted.internet import defer
 
-from ._base import SQLBaseStore
+from .background_updates import BackgroundUpdateStore
 
 
 logger = logging.getLogger(__name__)
 
 
-class DeviceInboxStore(SQLBaseStore):
+class DeviceInboxStore(BackgroundUpdateStore):
+    DEVICE_INBOX_STREAM_ID = "device_inbox_stream_drop"
+
+    def __init__(self, hs):
+        super(DeviceInboxStore, self).__init__(hs)
+
+        self.register_background_index_update(
+            "device_inbox_stream_index",
+            index_name="device_inbox_stream_id_user_id",
+            table="device_inbox",
+            columns=["stream_id", "user_id"],
+        )
+
+        self.register_background_update_handler(
+            self.DEVICE_INBOX_STREAM_ID,
+            self._background_drop_index_device_inbox,
+        )
 
     @defer.inlineCallbacks
     def add_messages_to_device_inbox(self, local_messages_by_user_then_device,
@@ -368,3 +384,21 @@ class DeviceInboxStore(SQLBaseStore):
             "delete_device_msgs_for_remote",
             delete_messages_for_remote_destination_txn
         )
+
+    @defer.inlineCallbacks
+    def _background_drop_index_device_inbox(self, progress, batch_size):
+        def reindex_txn(conn):
+            conn.set_session(autocommit=True)
+            try:
+                txn = conn.cursor()
+                txn.execute(
+                    "DROP INDEX IF EXISTS device_inbox_stream_id"
+                )
+            finally:
+                conn.set_session(autocommit=False)
+
+        yield self.runWithConnection(reindex_txn)
+
+        yield self._end_background_update(self.DEVICE_INBOX_STREAM_ID)
+
+        defer.returnValue(1)
diff --git a/synapse/storage/prepare_database.py b/synapse/storage/prepare_database.py
index e46ae6502e..b357f22be7 100644
--- a/synapse/storage/prepare_database.py
+++ b/synapse/storage/prepare_database.py
@@ -25,7 +25,7 @@ logger = logging.getLogger(__name__)
 
 # Remember to update this number every time a change is made to database
 # schema files, so the users will be informed on server restarts.
-SCHEMA_VERSION = 39
+SCHEMA_VERSION = 40
 
 dir_path = os.path.abspath(os.path.dirname(__file__))
 
diff --git a/synapse/storage/schema/delta/40/device_inbox.sql b/synapse/storage/schema/delta/40/device_inbox.sql
new file mode 100644
index 0000000000..ce58fe2082
--- /dev/null
+++ b/synapse/storage/schema/delta/40/device_inbox.sql
@@ -0,0 +1,20 @@
+/* Copyright 2016 OpenMarket 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.
+ */
+
+INSERT into background_updates (update_name, progress_json)
+    VALUES ('device_inbox_stream_index', '{}');
+
+INSERT into background_updates (update_name, progress_json, depends_on)
+    VALUES ('device_inbox_stream_drop', '{}', 'device_inbox_stream_index');