diff --git a/code_review_graph/graph.py b/code_review_graph/graph.py
index 2dfa97fc..ea2fa6fe 100644
--- a/code_review_graph/graph.py
+++ b/code_review_graph/graph.py
@@ -236,6 +236,11 @@ 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."""
+        # Flush any pending implicit transaction opened by earlier DML on this
+        # connection so the explicit BEGIN IMMEDIATE below doesn't trip SQLite's
+        # "cannot start a transaction within a transaction" error.
+        if self._conn.in_transaction:
+            self._conn.commit()
         self._conn.execute("BEGIN IMMEDIATE")
         try:
             self.remove_file_data(file_path)
diff --git a/code_review_graph/incremental.py b/code_review_graph/incremental.py
index 863211bb..f67e894c 100644
--- a/code_review_graph/incremental.py
+++ b/code_review_graph/incremental.py
@@ -352,8 +352,13 @@ def full_build(repo_root: Path, store: GraphStore) -> dict:
     # Purge stale data from files no longer on disk
     existing_files = set(store.get_all_files())
     current_abs = {str(repo_root / f) for f in files}
-    for stale in existing_files - current_abs:
-        store.remove_file_data(stale)
+    stale_files = existing_files - current_abs
+    if stale_files:
+        for stale in stale_files:
+            store.remove_file_data(stale)
+        # Commit the implicit transaction opened by the DELETEs so the
+        # subsequent BEGIN IMMEDIATE in store_file_nodes_edges succeeds.
+        store.commit()
 
     total_nodes = 0
     total_edges = 0
diff --git a/tests/test_graph.py b/tests/test_graph.py
index 5923f578..5ea757cb 100644
--- a/tests/test_graph.py
+++ b/tests/test_graph.py
@@ -107,6 +107,25 @@ 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_after_dangling_dml(self):
+        """Regression: store_file_nodes_edges must recover when the connection
+        is already inside an implicit transaction opened by a prior DML (e.g.
+        the stale-file purge loop in full_build). Previously this raised
+        'cannot start a transaction within a transaction'.
+        """
+        # Simulate the purge loop: run DELETEs without committing so the
+        # connection is left in an implicit transaction.
+        self.store.upsert_node(self._make_file_node("/stale.py"))
+        self.store.commit()
+        self.store.remove_file_data("/stale.py")
+        assert self.store._conn.in_transaction
+
+        nodes = [self._make_file_node(), self._make_func_node()]
+        # Should not raise sqlite3.OperationalError.
+        self.store.store_file_nodes_edges("/test/file.py", nodes, [])
+
+        assert len(self.store.get_nodes_by_file("/test/file.py")) == 2
+
     def test_search_nodes(self):
         self.store.upsert_node(self._make_func_node("authenticate"))
         self.store.upsert_node(self._make_func_node("authorize"))