diff --git a/code_review_graph/graph.py b/code_review_graph/graph.py
index 2dfa97f..2fa5c29 100644
--- a/code_review_graph/graph.py
+++ b/code_review_graph/graph.py
@@ -236,6 +236,13 @@ 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 implicit transaction started by prior DML (e.g.
+        # remove_file_data DELETEs during incremental_update/full_build).
+        # Python sqlite3 auto-begins a DEFERRED transaction on the first
+        # DML; BEGIN IMMEDIATE inside an active transaction raises
+        # OperationalError.  See GitHub issue #135.
+        if self._conn.in_transaction:
+            self._conn.commit()
         self._conn.execute("BEGIN IMMEDIATE")
         try:
             self.remove_file_data(file_path)
diff --git a/tests/test_graph.py b/tests/test_graph.py
index 5923f57..8a2641f 100644
--- a/tests/test_graph.py
+++ b/tests/test_graph.py
@@ -242,3 +242,29 @@ def test_empty_changed_files(self):
         assert result["changed_nodes"] == []
         assert result["impacted_nodes"] == []
         assert result["total_impacted"] == 0
+
+    def test_store_after_remove_no_transaction_error(self):
+        """Regression test for #135: remove_file_data then store_file_nodes_edges
+        must not raise 'cannot start a transaction within a transaction'."""
+        file_a = "/proj/a.py"
+        file_b = "/proj/b.py"
+        node_a = NodeInfo(
+            kind="File", name=file_a, file_path=file_a,
+            line_start=1, line_end=10, language="python",
+        )
+        node_b = NodeInfo(
+            kind="File", name=file_b, file_path=file_b,
+            line_start=1, line_end=10, language="python",
+        )
+        # Populate both files
+        self.store.store_file_nodes_edges(file_a, [node_a], [], "aaa")
+        self.store.store_file_nodes_edges(file_b, [node_b], [], "bbb")
+
+        # Simulate incremental_update: delete file_a, then re-store file_b
+        self.store.remove_file_data(file_a)
+        # This must not raise sqlite3.OperationalError
+        self.store.store_file_nodes_edges(file_b, [node_b], [], "ccc")
+
+        # Verify: file_a gone, file_b present
+        assert self.store.get_nodes_by_file(file_a) == []
+        assert len(self.store.get_nodes_by_file(file_b)) == 1
diff --git a/tests/test_incremental.py b/tests/test_incremental.py
index d7b3992..eeb9b51 100644
--- a/tests/test_incremental.py
+++ b/tests/test_incremental.py
@@ -241,6 +241,64 @@ def test_incremental_deleted_file(self, tmp_path):
             store.close()
 
 
+    def test_incremental_deleted_and_modified_files(self, tmp_path):
+        """Regression test for #135: incremental update with a mix of deleted
+        and modified files must not raise 'cannot start a transaction within
+        a transaction'."""
+        db_path = tmp_path / "test.db"
+        store = GraphStore(db_path)
+        try:
+            # Create two files and build them into the graph
+            a = tmp_path / "a.py"
+            b = tmp_path / "b.py"
+            a.write_text("def fa():\n    pass\n")
+            b.write_text("def fb():\n    pass\n")
+            incremental_update(tmp_path, store, changed_files=["a.py", "b.py"])
+            assert len(store.get_nodes_by_file(str(a))) > 0
+            assert len(store.get_nodes_by_file(str(b))) > 0
+
+            # Delete a.py, modify b.py, then do incremental update
+            a.unlink()
+            b.write_text("def fb_v2():\n    return 42\n")
+            # This must not raise sqlite3.OperationalError
+            incremental_update(
+                tmp_path, store, changed_files=["a.py", "b.py"]
+            )
+            # a.py removed, b.py updated
+            assert store.get_nodes_by_file(str(a)) == []
+            assert len(store.get_nodes_by_file(str(b))) > 0
+        finally:
+            store.close()
+
+    def test_full_build_stale_files_then_parse(self, tmp_path):
+        """Regression test for #135: full_build removing stale files then
+        parsing remaining files must not raise transaction errors."""
+        (tmp_path / ".git").mkdir()
+        db_path = tmp_path / "test.db"
+        store = GraphStore(db_path)
+        try:
+            # Pre-populate with a file that will become stale
+            stale = tmp_path / "stale.py"
+            stale.write_text("x = 1\n")
+            mock_target = "code_review_graph.incremental.get_all_tracked_files"
+            with patch(mock_target, return_value=["stale.py"]):
+                full_build(tmp_path, store)
+            assert len(store.get_nodes_by_file(str(stale))) > 0
+
+            # Remove stale.py, add fresh.py
+            stale.unlink()
+            fresh = tmp_path / "fresh.py"
+            fresh.write_text("def new_func():\n    pass\n")
+            with patch(mock_target, return_value=["fresh.py"]):
+                # This must not raise sqlite3.OperationalError
+                result = full_build(tmp_path, store)
+            assert result["files_parsed"] == 1
+            assert store.get_nodes_by_file(str(stale)) == []
+            assert len(store.get_nodes_by_file(str(fresh))) > 0
+        finally:
+            store.close()
+
+
 class TestParallelParsing:
     def test_parse_single_file(self, tmp_path):
         py_file = tmp_path / "single.py"