diff --git a/monkey_island/cc/resources/root.py b/monkey_island/cc/resources/root.py
index cf597bb69..9983ecc82 100644
--- a/monkey_island/cc/resources/root.py
+++ b/monkey_island/cc/resources/root.py
@@ -36,7 +36,8 @@ class Root(flask_restful.Resource):
 
     @staticmethod
     def reset_db():
-        [mongo.db[x].drop() for x in mongo.db.collection_names()]
+        # We can't drop system collections.
+        [mongo.db[x].drop() for x in mongo.db.collection_names() if not x.startswith('system.')]
         ConfigService.init_config()
         return jsonify(status='OK')