diff --git a/airflow-core/src/airflow/models/asset.py b/airflow-core/src/airflow/models/asset.py
index 8b28f2bea6184..650cb8589b424 100644
--- a/airflow-core/src/airflow/models/asset.py
+++ b/airflow-core/src/airflow/models/asset.py
@@ -108,12 +108,17 @@ def remove_references_to_deleted_dags(session: Session):
         DagScheduleAssetAliasReference,
         TaskOutletAssetReference,
     ]
-    for model in models_to_check:
-        session.execute(
-            delete(model)
-            .where(model.dag_id.in_(select(DagModel.dag_id).where(DagModel.is_stale)))
-            .execution_options(synchronize_session="fetch")
-        )
+
+    # The queries need to be done in separate steps, because in the case of multiple
+    # dag processors on MySQL, there could be a deadlock caused by acquiring both an
+    # exclusive lock for deletion and shared lock for query in reverse sequence
+    if stale_dag_ids := session.scalars(select(DagModel.dag_id).where(DagModel.is_stale)).all():
+        for model in models_to_check:
+            session.execute(
+                delete(model)
+                .where(model.dag_id.in_(stale_dag_ids))
+                .execution_options(synchronize_session="fetch")
+            )
 
 
 alias_association_table = Table(