diff --git a/lib/galaxy/workflow/refactor/execute.py b/lib/galaxy/workflow/refactor/execute.py
index fc38a9351468..264fa843d830 100644
--- a/lib/galaxy/workflow/refactor/execute.py
+++ b/lib/galaxy/workflow/refactor/execute.py
@@ -531,6 +531,9 @@ def _patch_step(self, execution, step, step_def):
                 if upgrade_input["name"] == input_name:
                     matching_input = upgrade_input
                     break
+                elif step.when_expression and f"inputs.{input_name}" in step.when_expression:
+                    # TODO: eventually track step inputs more formally
+                    matching_input = upgrade_input
 
             # In the future check parameter type, format, mapping status...
             if matching_input is None:
diff --git a/test/integration/test_workflow_refactoring.py b/test/integration/test_workflow_refactoring.py
index d2501090aeef..d68b8916145b 100644
--- a/test/integration/test_workflow_refactoring.py
+++ b/test/integration/test_workflow_refactoring.py
@@ -548,9 +548,11 @@ def test_tool_version_upgrade_keeps_when_expression(self):
   the_step:
     tool_id: multiple_versions
     tool_version: '0.1'
+    in:
+      when: the_bool
     state:
       inttest: 0
-    when: $inputs.the_bool
+    when: $(inputs.when)
 """
         )
         assert self._latest_workflow.step_by_label("the_step").tool_version == "0.1"