diff --git a/connectors/keboola/extractor.py b/connectors/keboola/extractor.py
index 40d172a..629a5d5 100644
--- a/connectors/keboola/extractor.py
+++ b/connectors/keboola/extractor.py
@@ -146,13 +146,22 @@ def run(output_dir: str, table_configs: List[Dict[str, Any]], keboola_url: str,
                 pass
 
     finally:
+        conn.execute("CHECKPOINT")
         conn.close()
 
-    # Atomic replace: swap temp DB into place
+    # Atomic replace: swap temp DB into place, cleaning up any WAL files
     import shutil
+    old_wal = Path(str(db_path) + ".wal")
+    if old_wal.exists():
+        old_wal.unlink()
+
     if tmp_db_path.exists():
         shutil.move(str(tmp_db_path), str(db_path))
 
+    tmp_wal = Path(str(tmp_db_path) + ".wal")
+    if tmp_wal.exists():
+        tmp_wal.unlink()
+
     return stats
 
 
diff --git a/src/orchestrator.py b/src/orchestrator.py
index e8e7e78..6bd3efc 100644
--- a/src/orchestrator.py
+++ b/src/orchestrator.py
@@ -42,6 +42,27 @@ def _validate_identifier(name: str, context: str) -> bool:
     return True
 
 
+def _atomic_swap_db(tmp_path: str, target_path: str) -> None:
+    """Atomically replace target DuckDB file, cleaning up WAL files."""
+    import shutil
+    target = Path(target_path)
+    tmp = Path(tmp_path)
+
+    # Remove old WAL file if it exists
+    old_wal = Path(str(target) + ".wal")
+    if old_wal.exists():
+        old_wal.unlink()
+
+    # Move temp DB into place
+    if tmp.exists():
+        shutil.move(str(tmp), str(target))
+
+    # Clean up temp WAL
+    tmp_wal = Path(str(tmp) + ".wal")
+    if tmp_wal.exists():
+        tmp_wal.unlink()
+
+
 def _get_extracts_dir() -> Path:
     data_dir = Path(os.environ.get("DATA_DIR", "./data"))
     return data_dir / "extracts"
@@ -118,12 +139,11 @@ class SyncOrchestrator:
                     result[ext_dir.name] = tables
                     logger.info("Attached %s: %d tables", ext_dir.name, len(tables))
         finally:
+            conn.execute("CHECKPOINT")
             conn.close()
 
         # Atomic swap: replace analytics.duckdb with new version
-        import shutil
-        if Path(tmp_path).exists():
-            shutil.move(tmp_path, self._db_path)
+        _atomic_swap_db(tmp_path, self._db_path)
 
         return result
 
diff --git a/tests/test_orchestrator.py b/tests/test_orchestrator.py
index 8a903eb..d54507a 100644
--- a/tests/test_orchestrator.py
+++ b/tests/test_orchestrator.py
@@ -333,6 +333,32 @@ class TestSyncOrchestrator:
         # The safe source must still be processed
         assert "keboola" in result
 
+    def test_rebuild_cleans_wal_files(self, setup_env):
+        """No .wal files should remain after rebuild completes."""
+        from src.orchestrator import SyncOrchestrator
+
+        _create_mock_extract(
+            setup_env["extracts_dir"],
+            "keboola",
+            [{"name": "orders", "data": [{"id": "1", "total": "100"}]}],
+        )
+
+        analytics_db = setup_env["analytics_db"]
+        orch = SyncOrchestrator(analytics_db_path=analytics_db)
+
+        # Simulate a pre-existing WAL file for the target analytics DB
+        wal_path = Path(analytics_db + ".wal")
+        wal_path.write_text("stale wal")
+        assert wal_path.exists(), "Pre-condition: WAL file should exist before rebuild"
+
+        orch.rebuild()
+
+        # After rebuild, no WAL files should remain alongside the analytics DB
+        assert not wal_path.exists(), "Old WAL file must be removed during atomic swap"
+        # Also verify no temp WAL was left behind
+        tmp_wal = Path(analytics_db + ".tmp.wal")
+        assert not tmp_wal.exists(), "Temp WAL file must be cleaned up"
+
     def test_rejects_malicious_table_name(self, setup_env):
         """Tables with SQL injection names in _meta must be skipped; safe tables still work."""
         from src.orchestrator import SyncOrchestrator