diff --git a/xarray_ms/backend/msv2/entrypoint.py b/xarray_ms/backend/msv2/entrypoint.py
index 9764f92..becb5e5 100644
--- a/xarray_ms/backend/msv2/entrypoint.py
+++ b/xarray_ms/backend/msv2/entrypoint.py
@@ -364,6 +364,7 @@ def open_datatree(
     if not partition_chunks:
       partition_chunks = kwargs.pop("chunks", None)
     elif "chunks" in kwargs:
+      kwargs.pop("chunks", None)
       warnings.warn("`partition_chunks` overriding `chunks`")
 
     pchunks = promote_chunks(structure, partition_chunks)