diff --git a/code_review_graph/graph.py b/code_review_graph/graph.py
index 2dfa97fc..4b2b496b 100644
--- a/code_review_graph/graph.py
+++ b/code_review_graph/graph.py
@@ -236,16 +236,28 @@ def store_file_nodes_edges(
         self, file_path: str, nodes: list[NodeInfo], edges: list[EdgeInfo], fhash: str = ""
     ) -> None:
         """Atomically replace all data for a file."""
-        self._conn.execute("BEGIN IMMEDIATE")
+        savepoint = "__crg_store_file_nodes_edges__"
+        use_savepoint = self._conn.in_transaction
+        if use_savepoint:
+            self._conn.execute(f"SAVEPOINT {savepoint}")  # nosec B608
+        else:
+            self._conn.execute("BEGIN IMMEDIATE")
         try:
             self.remove_file_data(file_path)
             for node in nodes:
                 self.upsert_node(node, file_hash=fhash)
             for edge in edges:
                 self.upsert_edge(edge)
-            self._conn.commit()
+            if use_savepoint:
+                self._conn.execute(f"RELEASE SAVEPOINT {savepoint}")  # nosec B608
+            else:
+                self._conn.commit()
         except BaseException:
-            self._conn.rollback()
+            if use_savepoint:
+                self._conn.execute(f"ROLLBACK TO SAVEPOINT {savepoint}")  # nosec B608
+                self._conn.execute(f"RELEASE SAVEPOINT {savepoint}")  # nosec B608
+            else:
+                self._conn.rollback()
             raise
         self._invalidate_cache()
 
diff --git a/tests/test_graph.py b/tests/test_graph.py
index 5923f578..bb253fbb 100644
--- a/tests/test_graph.py
+++ b/tests/test_graph.py
@@ -107,6 +107,24 @@ def test_store_file_nodes_edges(self):
         result = self.store.get_nodes_by_file("/test/file.py")
         assert len(result) == 2
 
+    def test_store_file_nodes_edges_with_existing_transaction(self):
+        """File replacement should work even if the caller already opened a transaction."""
+        self.store.upsert_node(self._make_file_node("/test/other.py"))
+        nodes = [self._make_file_node(), self._make_func_node()]
+        edges = [
+            EdgeInfo(
+                kind="CONTAINS", source="/test/file.py",
+                target="/test/file.py::my_func", file_path="/test/file.py",
+            )
+        ]
+
+        self.store.store_file_nodes_edges("/test/file.py", nodes, edges)
+        self.store.commit()
+
+        result = self.store.get_nodes_by_file("/test/file.py")
+        assert len(result) == 2
+        assert self.store.get_node("/test/other.py") is not None
+
     def test_search_nodes(self):
         self.store.upsert_node(self._make_func_node("authenticate"))
         self.store.upsert_node(self._make_func_node("authorize"))