diff --git a/bento/io/_index.py b/bento/io/_index.py
index 4a2f378..d7b78da 100644
--- a/bento/io/_index.py
+++ b/bento/io/_index.py
@@ -121,6 +121,7 @@ def _sjoin_shapes(sdata: SpatialData, instance_key: str, shape_keys: List[str]):
             )
             .rename(columns={"index_right": shape_key})
         )
+        parent_shape[shape_key] = parent_shape[shape_key].fillna("")
 
         # Save shape index as column in instance_key shape
         set_shape_metadata(