diff --git a/synapse/storage/search.py b/synapse/storage/search.py
index f7730f5d7..1baed674a 100644
--- a/synapse/storage/search.py
+++ b/synapse/storage/search.py
@@ -158,6 +158,13 @@ class SearchStore(BackgroundUpdateStore):
                 )
                 conn.set_session(autocommit=False)
 
+                pg = dict(progress)
+                pg["have_added_indexes"] = True
+
+                self._background_update_progress_txn(
+                    conn.cursor(), self.EVENT_SEARCH_ORDER_UPDATE_NAME, progress
+                )
+
             yield self.runWithConnection(create_index)
 
         INSERT_CLUMP_SIZE = 1000