diff --git a/synapse/storage/schema/delta/v12.sql b/synapse/storage/schema/delta/v12.sql
index 302d958dbf..b87ef1fe79 100644
--- a/synapse/storage/schema/delta/v12.sql
+++ b/synapse/storage/schema/delta/v12.sql
@@ -63,3 +63,5 @@ CREATE TABLE IF NOT EXISTS user_filters(
 CREATE INDEX IF NOT EXISTS user_filters_by_user_id_filter_id ON user_filters(
   user_id, filter_id
 );
+
+PRAGMA user_version = 12;