diff --git a/src/spatialdata/_core/query/relational_query.py b/src/spatialdata/_core/query/relational_query.py
index 1a672eefc..94c4fcd65 100644
--- a/src/spatialdata/_core/query/relational_query.py
+++ b/src/spatialdata/_core/query/relational_query.py
@@ -191,7 +191,7 @@ def _get_joined_table_indices(
     -------
         The indices that of the table that match the SpatialElement indices.
     """
-    mask = np.isin(table_instance_key_column.to_numpy(), element_indices)
+    mask = table_instance_key_column.isin(element_indices).to_numpy()
     if joined_indices is None:
         if match_rows == "left":
             _, joined_indices = _match_rows(table_instance_key_column, mask, element_indices, match_rows)
@@ -232,7 +232,7 @@ def _get_masked_element(
     -------
     The masked spatial element based on the provided indices and match rows.
     """
-    mask = np.isin(table_instance_key_column.to_numpy(), element_indices)
+    mask = table_instance_key_column.isin(element_indices).to_numpy()
     masked_table_instance_key_column = table_instance_key_column[mask]
     mask_values: NDArray[Any] | pd.Index | None = (
         masked_values if len(masked_values := masked_table_instance_key_column.to_numpy()) != 0 else None