diff --git a/lib/galaxy/webapps/galaxy/services/wes.py b/lib/galaxy/webapps/galaxy/services/wes.py
index 3d3ac701847..02837ed8702 100644
--- a/lib/galaxy/webapps/galaxy/services/wes.py
+++ b/lib/galaxy/webapps/galaxy/services/wes.py
@@ -493,7 +493,11 @@ class WesService(ServiceBase):
             )
 
             # Use the existing workflow directly - no need to create a new one
-            # Skip to step 5 (engine parameters and history)
+            if instance:
+                # The URI named a specific version - invoke that one, not the latest.
+                invoke_workflow_id = trans.security.decode_id(encoded_workflow_id)
+            else:
+                invoke_workflow_id = stored_workflow.id
         else:
             # Step 2: Determine/validate workflow type
             detected_type = _determine_workflow_type(workflow_dict)
@@ -520,6 +524,8 @@ class WesService(ServiceBase):
                 source="WES API",
             )
             stored_workflow = created_workflow.stored_workflow
+            invoke_workflow_id = stored_workflow.id
+            instance = False
 
         # Step 5: Parse engine parameters and create/select history
         engine_params = {}
@@ -532,9 +538,10 @@ class WesService(ServiceBase):
         history = _get_or_create_history(trans, engine_params)
 
         # Step 6: Parse workflow parameters
-        invoke_params = {
+        invoke_params: dict[str, Any] = {
             "history_id": trans.security.encode_id(history.id),
             "inputs_by": "name",
+            "instance": instance,
         }
 
         if workflow_params:
@@ -554,7 +561,7 @@ class WesService(ServiceBase):
         invoke_payload = InvokeWorkflowPayload(**invoke_params)
         workflow_invocation_response = self._workflows_service.invoke_workflow(
             trans,
-            trans.security.encode_id(stored_workflow.id),
+            invoke_workflow_id,
             invoke_payload,
         )
 
diff --git a/lib/galaxy_test/api/test_wes.py b/lib/galaxy_test/api/test_wes.py
index 4eba1a99748..af35bc7651d 100644
--- a/lib/galaxy_test/api/test_wes.py
+++ b/lib/galaxy_test/api/test_wes.py
@@ -520,16 +520,23 @@ steps:
             self._assert_status_code_is(response, 200)
 
     def test_wes_submit_run_with_gxworkflow_uri_with_instance_param(self):
-        """Test gxworkflow:// URI with instance=true parameter."""
+        """Test gxworkflow:// URI with instance=true runs that version, not the latest."""
         with self.dataset_populator.test_history() as history_id:
             dataset_id = self._get_test_dataset_id(history_id)
 
             # Upload a workflow to get its ID
             workflow_id = self._upload_yaml_workflow(WORKFLOW_SIMPLE)
-            latest_instance_id = self._latest_instance_id(workflow_id, history_id)
+            first_instance_id = self._latest_instance_id(workflow_id, history_id)
+
+            # Create a second version so the referenced instance is no longer the latest
+            workflow_object = self._download_workflow(workflow_id)
+            workflow_object["steps"]["1"]["annotation"] = "second version"
+            update_response = self.workflow_populator.update_workflow(workflow_id, workflow_object)
+            self._assert_status_code_is(update_response, 200)
+            assert self._latest_instance_id(workflow_id, history_id) != first_instance_id
 
             # Construct gxworkflow:// URI with instance=true
-            workflow_uri = f"gxworkflow://{latest_instance_id}?instance=true"
+            workflow_uri = f"gxworkflow://{first_instance_id}?instance=true"
 
             # Submit workflow using the gxworkflow:// URI
             data = {
@@ -545,6 +552,8 @@ steps:
 
             # Validate response
             assert run_id is not None
+            invocation = self.workflow_populator.get_invocation(run_id)
+            assert invocation["workflow_id"] == first_instance_id
 
     def test_wes_submit_run_with_gxworkflow_uri_published_workflow(self):
         """A published workflow owned by another user can be run via gxworkflow://."""