diff --git a/tests/storage/test_id_generators.py b/tests/storage/test_id_generators.py
index 051c5de44d..c8cdd9ed53 100644
--- a/tests/storage/test_id_generators.py
+++ b/tests/storage/test_id_generators.py
@@ -78,7 +78,7 @@ class MultiWriterIdGeneratorBase(HomeserverTestCase):
         writers: list[str] | None = None,
     ) -> MultiWriterIdGenerator:
         def _create(conn: LoggingDatabaseConnection) -> MultiWriterIdGenerator:
-            return MultiWriterIdGenerator(
+            id_gen = MultiWriterIdGenerator(
                 db_conn=conn,
                 db=self.db_pool,
                 notifier=self.hs.get_replication_notifier(),
@@ -90,6 +90,15 @@ class MultiWriterIdGeneratorBase(HomeserverTestCase):
                 writers=writers or ["master"],
                 positive=self.positive,
             )
+            # Constructing the generator prunes stale `stream_positions` rows
+            # (writers no longer in the config); commit so that persists for the
+            # next generator we create. Without this the test relies on the
+            # connection pool keeping the uncommitted transaction open and
+            # visible across `runWithConnection` calls, which adbapi happens to
+            # do (one connection per thread) but the native pool does not (a
+            # fresh connection each call, rolled back if left mid-transaction).
+            conn.commit()
+            return id_gen
 
         self.instances[instance_name] = self.get_success_or_raise(
             self.db_pool.runWithConnection(_create)