diff --git a/airflow/utils/db.py b/airflow/utils/db.py
index 9088823de3589..54aacc4d2276a 100644
--- a/airflow/utils/db.py
+++ b/airflow/utils/db.py
@@ -1292,6 +1292,7 @@ class BadReferenceConfig:
 
     ti_lkp_table = _create_ti_key_lkp_table(session=session, table_name='_airflow_tmp_ti_key_lkp')
 
+    session.commit()
     for model, change_version, bad_ref_cfg in models_list:
         log.debug("checking model %s", model.__tablename__)
         # We can't use the model here since it may differ from the db state due to
@@ -1304,11 +1305,13 @@ class BadReferenceConfig:
         if "run_id" in source_table.columns:
             continue
 
+        session.commit()
         bad_rows_subquery = bad_ref_cfg.exists_func(session, source_table, ti_lkp_table=ti_lkp_table)
         dangling_table_name = _format_airflow_moved_table_name(source_table.name, change_version, 'dangling')
         select_list = [x.label(x.name) for x in source_table.c]
         log.debug(bad_rows_subquery.selectable.compile())
         invalid_rows_query = session.query(*select_list).filter(~bad_rows_subquery.exists())
+        session.commit()
         if dangling_table_name in existing_table_names:
             invalid_row_count = invalid_rows_query.count()
             if invalid_row_count <= 0:
@@ -1330,6 +1333,7 @@ class BadReferenceConfig:
             dangling_table_name,
         )
         session.commit()
+    session.commit()
     ti_lkp_table.drop(bind=settings.engine, checkfirst=True)