diff --git a/bento/geometry/_ops.py b/bento/geometry/_ops.py
index bc600fa..c66da9a 100644
--- a/bento/geometry/_ops.py
+++ b/bento/geometry/_ops.py
@@ -49,7 +49,8 @@ def overlay(
     shape1 = sdata[s1]
     shape2 = sdata[s2]
 
-    new_shape = shape1.overlay(shape2, how=how, make_valid=make_valid)
+    new_shape = shape1.overlay(shape2, how=how, make_valid=make_valid)[["geometry"]]
+    new_shape.index = new_shape.index.astype(str)
     new_shape.attrs = {}
 
     transform = shape1.attrs
diff --git a/bento/io/_index.py b/bento/io/_index.py
index 903f8a8..c730dfd 100644
--- a/bento/io/_index.py
+++ b/bento/io/_index.py
@@ -124,6 +124,7 @@ def _sjoin_shapes(
                 .dissolve(by="index_right", observed=True, dropna=False)
                 .reset_index(drop=True)[["geometry"]]
             )
+            child_shape.index = child_shape.index.astype(str)
             child_shape = ShapesModel.parse(child_shape)
             child_shape.attrs = child_attrs
             sdata.shapes[shape_key] = child_shape
diff --git a/bento/io/_io.py b/bento/io/_io.py
index 4ef7117..431df92 100644
--- a/bento/io/_io.py
+++ b/bento/io/_io.py
@@ -78,18 +78,10 @@ def prep(
     sdata.points[points_key].attrs["spatialdata_attrs"]["instance_key"] = instance_key
 
     pbar = tqdm(total=3)
-    if len(point_sjoin) > 0:
-        pbar.set_description("Mapping points")
-        sdata = _sjoin_points(
-            sdata=sdata,
-            points_key=points_key,
-            shape_keys=point_sjoin,
-        )
-
-    pbar.update()
-
     if len(shape_sjoin) > 0:
-        pbar.set_description("Mapping shapes")
+        pbar.set_description(
+            "Mapping shapes"
+        )  # Map shapes must happen first; manyto1 mapping resets shape index
         sdata = _sjoin_shapes(
             sdata=sdata,
             instance_key=instance_key,
@@ -99,6 +91,16 @@ def prep(
 
     pbar.update()
 
+    if len(point_sjoin) > 0:
+        pbar.set_description("Mapping points")
+        sdata = _sjoin_points(
+            sdata=sdata,
+            points_key=points_key,
+            shape_keys=point_sjoin,
+        )
+
+    pbar.update()
+
     # Only keep points within instance_key shape
     _sync_points(sdata, points_key)