diff --git a/datasette/app.py b/datasette/app.py
index 1f9e9d3009..5dc15083f5 100644
--- a/datasette/app.py
+++ b/datasette/app.py
@@ -454,7 +454,7 @@ async def apply_metadata_json(self):
         # step 2: database-level metadata
         for dbname, db in self._metadata_local.get("databases", {}).items():
             for key, value in db.items():
-                if key == "tables":
+                if key in ("tables", "queries"):
                     continue
                 await self.set_database_metadata(dbname, key, value)