diff --git a/apis/python/src/tiledbsc/soma_slice.py b/apis/python/src/tiledbsc/soma_slice.py
index b9165a6800..e33d17eaa2 100644
--- a/apis/python/src/tiledbsc/soma_slice.py
+++ b/apis/python/src/tiledbsc/soma_slice.py
@@ -105,17 +105,29 @@ def to_anndata(self) -> ad.AnnData:
             if isinstance(data, pd.DataFrame):
                 # Make obs_id and var_id accessible as columns.
                 data = data.reset_index()
+
                 data = util.X_and_ids_to_sparse_matrix(
                     data,
                     "obs_id",  # row_dim_name
                     "var_id",  # col_dim_name
                     "value",  # attr_name
-                    self.obs.index,
-                    self.var.index,
+                    obs.index,
+                    var.index,
                 )
+
             if isinstance(data, pa.Table):
                 data = data.to_pandas()
                 data.set_index(["obs_id", "var_id"], inplace=True)
+
+                data = util.X_and_ids_to_sparse_matrix(
+                    data,
+                    "obs_id",  # row_dim_name
+                    "var_id",  # col_dim_name
+                    "value",  # attr_name
+                    obs.index,
+                    var.index,
+                )
+
             # We use AnnData as our in-memory storage. For SOMAs, all X layers are arrays within the
             # soma.X group; for AnnData, the 'data' layer is ann.X and all the others are in
             # ann.layers.
diff --git a/apis/python/tests/test_soco_slice_query.py b/apis/python/tests/test_soco_slice_query.py
index 05e9782577..c494a3a2c4 100644
--- a/apis/python/tests/test_soco_slice_query.py
+++ b/apis/python/tests/test_soco_slice_query.py
@@ -37,33 +37,37 @@ def test_soco_slice_query(tmp_path):
     var_attrs = ["feature_name"]
     var_query_string = 'feature_name == "MT-CO3"'
 
-    soma_slices = []
-    for soma in soco:
-        # E.g. querying for 'cell_type == "blood"' but this SOMA doesn't have a cell_type column in
-        # its obs at all.
-        if not soma.obs.has_attr_names(obs_attrs):
-            continue
-        # E.g. querying for 'feature_name == "MT-CO3"' but this SOMA doesn't have a feature_name
-        # column in its var at all.
-        if not soma.var.has_attr_names(var_attrs):
-            continue
-
-        # The return_arrow=True case drives arrow-format all the way through SOMA, SOMASlice,
-        # obs, var, X, etc.
-        soma_slice = soma.query(
-            obs_query_string=obs_query_string, var_query_string=var_query_string
-        )
-        if soma_slice is not None:
-            soma_slices.append(soma_slice)
-
-    result_soma_slice = tiledbsc.SOMASlice.concat(soma_slices)
-    assert result_soma_slice is not None
-
-    ann = result_soma_slice.to_anndata()
-
-    assert ann.obs.shape == (400, 17)
-    assert ann.var.shape == (1, 3)
-    assert ann.X.shape == (400, 1)
+    # The return_arrow=True case drives Arrow format all the way through SOMA, SOMASlice,
+    # obs, var, X, etc.
+    for return_arrow in [False, True]:
+
+        soma_slices = []
+        for soma in soco:
+            # E.g. querying for 'cell_type == "blood"' but this SOMA doesn't have a cell_type column in
+            # its obs at all.
+            if not soma.obs.has_attr_names(obs_attrs):
+                continue
+            # E.g. querying for 'feature_name == "MT-CO3"' but this SOMA doesn't have a feature_name
+            # column in its var at all.
+            if not soma.var.has_attr_names(var_attrs):
+                continue
+
+            soma_slice = soma.query(
+                obs_query_string=obs_query_string,
+                var_query_string=var_query_string,
+                return_arrow=return_arrow,
+            )
+            if soma_slice is not None:
+                soma_slices.append(soma_slice)
+
+        result_soma_slice = tiledbsc.SOMASlice.concat(soma_slices)
+        assert result_soma_slice is not None
+
+        ann = result_soma_slice.to_anndata()
+
+        assert ann.obs.shape == (400, 17)
+        assert ann.var.shape == (1, 3)
+        assert ann.X.shape == (400, 1)
 
 
 def test_soco_slice_query_nans(tmp_path):