diff --git a/src/spatialdata_io/readers/xenium.py b/src/spatialdata_io/readers/xenium.py
index 5940ae3d..deea8914 100644
--- a/src/spatialdata_io/readers/xenium.py
+++ b/src/spatialdata_io/readers/xenium.py
@@ -468,6 +468,8 @@ def _get_labels_and_indices_mapping(
                     "label_index": real_label_index.astype(np.int64),
                 }
             )
+            # because AnnData converts the indices to str
+            indices_mapping.index = indices_mapping.index.astype(str)
             return labels, indices_mapping
 
 
@@ -497,6 +499,8 @@ def _get_cells_metadata_table_from_zarr(
 
             cell_id_str = cell_id_str_from_prefix_suffix_uint32(cell_id_prefix, dataset_suffix)
             df[XeniumKeys.CELL_ID] = cell_id_str
+            # because AnnData converts the indices to str
+            df.index = df.index.astype(str)
             return df