diff --git a/backend/app/pypi_proxy.py b/backend/app/pypi_proxy.py
index 3f18e67..f336c0c 100644
--- a/backend/app/pypi_proxy.py
+++ b/backend/app/pypi_proxy.py
@@ -524,6 +524,10 @@ async def pypi_download_file(
             )
             db.add(system_project)
             db.flush()
+        elif not system_project.is_system:
+            # Ensure existing project is marked as system
+            system_project.is_system = True
+            db.flush()
 
         # Normalize package name
         normalized_name = re.sub(r'[-_.]+', '-', package_name).lower()