diff --git a/sdks/python/apache_beam/runners/portability/fn_api_runner/translations.py b/sdks/python/apache_beam/runners/portability/fn_api_runner/translations.py
index 8f12779d67f8..b3d6e027b579 100644
--- a/sdks/python/apache_beam/runners/portability/fn_api_runner/translations.py
+++ b/sdks/python/apache_beam/runners/portability/fn_api_runner/translations.py
@@ -557,8 +557,14 @@ def add_parent(child, parent):
             pipeline_proto.components.transforms[parent])
         copy_output_pcollections(components.transforms[parent])
         del components.transforms[parent].subtransforms[:]
-        add_parent(parent, parents.get(parent))
+      # Ensure that child is the last item in the parent's subtransforms.
+      # If the stages were previously sorted into topological order using
+      # sort_stages, this ensures that the parent transforms are also
+      # added in topological order.
+      if child in components.transforms[parent].subtransforms:
+        components.transforms[parent].subtransforms.remove(child)
       components.transforms[parent].subtransforms.append(child)
+      add_parent(parent, parents.get(parent))
 
   def copy_subtransforms(transform):
     for subtransform_id in transform.subtransforms:
diff --git a/sdks/python/apache_beam/runners/portability/fn_api_runner/translations_test.py b/sdks/python/apache_beam/runners/portability/fn_api_runner/translations_test.py
index 0ce11bda45c4..8eb79609367d 100644
--- a/sdks/python/apache_beam/runners/portability/fn_api_runner/translations_test.py
+++ b/sdks/python/apache_beam/runners/portability/fn_api_runner/translations_test.py
@@ -186,6 +186,37 @@ def test_optimize_multiple_combine_globally(self):
     beam.Pipeline.from_runner_api(
         optimized_pipeline_proto, runner, pipeline_options.PipelineOptions())
 
+  def test_pipeline_from_sorted_stages_is_toplogically_ordered(self):
+    pipeline = beam.Pipeline()
+    side = pipeline | 'side' >> Create([3, 4])
+
+    class CreateAndMultiplyBySide(beam.PTransform):
+      def expand(self, pcoll):
+        return (
+            pcoll | 'main' >> Create([1, 2]) | 'compute' >> beam.FlatMap(
+                lambda x, s: [x * y for y in s], beam.pvalue.AsIter(side)))
+
+    _ = pipeline | 'create-and-multiply-by-side' >> CreateAndMultiplyBySide()
+    pipeline_proto = pipeline.to_runner_api()
+    optimized_pipeline_proto = translations.optimize_pipeline(
+        pipeline_proto, [
+            (lambda stages, _: reversed(list(stages))),
+            translations.sort_stages,
+        ],
+        known_runner_urns=frozenset(),
+        partial=True)
+
+    def assert_is_topologically_sorted(transform_id, visited_pcolls):
+      transform = optimized_pipeline_proto.components.transforms[transform_id]
+      self.assertTrue(set(transform.inputs.values()).issubset(visited_pcolls))
+      visited_pcolls.update(transform.outputs.values())
+      for subtransform in transform.subtransforms:
+        assert_is_topologically_sorted(subtransform, visited_pcolls)
+
+    self.assertEqual(len(optimized_pipeline_proto.root_transform_ids), 1)
+    assert_is_topologically_sorted(
+        optimized_pipeline_proto.root_transform_ids[0], set())
+
 
 if __name__ == '__main__':
   logging.getLogger().setLevel(logging.INFO)