diff --git a/src/spatialdata/_core/query/spatial_query.py b/src/spatialdata/_core/query/spatial_query.py
index 04473bb9..b0386cd2 100644
--- a/src/spatialdata/_core/query/spatial_query.py
+++ b/src/spatialdata/_core/query/spatial_query.py
@@ -761,11 +761,15 @@ def polygon_query(
     # TODO: the performance for this case can be greatly improved by using the geopandas queries only once, and not
     #  in a loop as done preliminarily here
     if points or images or labels:
-        raise NotImplementedError(
-            "points=True, images=True and labels=True are not implemented when querying by multiple polygons. "
-            "If you encounter this error, please"
-            " open an issue on GitHub and we will prioritize the implementation."
+        logger.warning(
+            "Spatial querying of images, points and labels is not implemented when querying by multiple polygons "
+            'simultaneously. You can silence this warning by setting "points=False, images=False, labels=False". If '
+            "you need this implementation please open an issue on GitHub and we will prioritize the implementation."
         )
+        points = False
+        images = False
+        labels = False
+
     sdatas = []
     for polygon in tqdm(polygons):
         try:
diff --git a/tests/core/query/test_spatial_query.py b/tests/core/query/test_spatial_query.py
index 29eeff5d..6db7e904 100644
--- a/tests/core/query/test_spatial_query.py
+++ b/tests/core/query/test_spatial_query.py
@@ -380,7 +380,11 @@ def test_polygon_query_shapes(sdata_query_aggregation):
     circle_pol = circle.buffer(sdata["by_circles"].radius.iloc[0])
 
     queried = polygon_query(
-        values_sdata, polygons=polygon, target_coordinate_system="global", shapes=True, points=False
+        values_sdata,
+        polygons=polygon,
+        target_coordinate_system="global",
+        shapes=True,
+        points=False,
     )
     assert len(queried["values_polygons"]) == 4
     assert len(queried["values_circles"]) == 4