diff --git a/synapse/storage/schema/delta/54/stats2.sql b/synapse/storage/schema/delta/54/stats2.sql
new file mode 100644
index 0000000000..3b2d48447f
--- /dev/null
+++ b/synapse/storage/schema/delta/54/stats2.sql
@@ -0,0 +1,28 @@
+/* Copyright 2019 The Matrix.org Foundation C.I.C.
+ *
+ * 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.
+ */
+
+-- This delta file gets run after `54/stats.sql` delta.
+
+-- We want to add some indices to the temporary stats table, so we re-insert
+-- 'populate_stats_createtables' if we are still processing the rooms update.
+INSERT INTO background_updates (update_name, progress_json)
+    SELECT 'populate_stats_createtables', '{}'
+    WHERE
+        'populate_stats_process_rooms' IN (
+            SELECT update_name FROM background_updates
+        )
+        AND 'populate_stats_createtables' NOT IN (  -- don't insert if already exists
+            SELECT update_name FROM background_updates
+        );
diff --git a/synapse/storage/stats.py b/synapse/storage/stats.py
index a99637d4b4..1c0b183a56 100644
--- a/synapse/storage/stats.py
+++ b/synapse/storage/stats.py
@@ -18,6 +18,7 @@ import logging
 from twisted.internet import defer
 
 from synapse.api.constants import EventTypes, Membership
+from synapse.storage.prepare_database import get_statements
 from synapse.storage.state_deltas import StateDeltasStore
 from synapse.util.caches.descriptors import cached
 
@@ -69,12 +70,25 @@ class StatsStore(StateDeltasStore):
 
         # Get all the rooms that we want to process.
         def _make_staging_area(txn):
-            sql = (
-                "CREATE TABLE IF NOT EXISTS "
-                + TEMP_TABLE
-                + "_rooms(room_id TEXT NOT NULL, events BIGINT NOT NULL)"
-            )
-            txn.execute(sql)
+            # Create the temporary tables
+            stmts = get_statements("""
+                -- We just recreate the table, we'll be reinserting the
+                -- correct entries again later anyway.
+                DROP TABLE IF EXISTS {temp}_rooms;
+
+                CREATE TABLE IF NOT EXISTS {temp}_rooms(
+                    room_id TEXT NOT NULL,
+                    events BIGINT NOT NULL
+                );
+
+                CREATE INDEX {temp}_rooms_events
+                    ON {temp}_rooms(events);
+                CREATE INDEX {temp}_rooms_id
+                    ON {temp}_rooms(room_id);
+            """.format(temp=TEMP_TABLE).splitlines())
+
+            for statement in stmts:
+                txn.execute(statement)
 
             sql = (
                 "CREATE TABLE IF NOT EXISTS "
@@ -83,15 +97,16 @@ class StatsStore(StateDeltasStore):
             )
             txn.execute(sql)
 
-            # Get rooms we want to process from the database
+            # Get rooms we want to process from the database, only adding
+            # those that we haven't (i.e. those not in room_stats_earliest_token)
             sql = """
-                SELECT room_id, count(*) FROM current_state_events
-                GROUP BY room_id
-            """
+                INSERT INTO %s_rooms (room_id, events)
+                SELECT c.room_id, count(*) FROM current_state_events AS c
+                LEFT JOIN room_stats_earliest_token AS t USING (room_id)
+                WHERE t.room_id IS NULL
+                GROUP BY c.room_id
+            """ % (TEMP_TABLE,)
             txn.execute(sql)
-            rooms = [{"room_id": x[0], "events": x[1]} for x in txn.fetchall()]
-            self._simple_insert_many_txn(txn, TEMP_TABLE + "_rooms", rooms)
-            del rooms
 
         new_pos = yield self.get_max_stream_id_in_current_state_deltas()
         yield self.runInteraction("populate_stats_temp_build", _make_staging_area)