diff --git a/cylc/flow/scheduler.py b/cylc/flow/scheduler.py
index 0d793997296..db55fae2494 100644
--- a/cylc/flow/scheduler.py
+++ b/cylc/flow/scheduler.py
@@ -1267,6 +1267,10 @@ def _configure_contact(self) -> None:
     def load_flow_file(self, is_reload=False):
         """Load, and log the workflow definition."""
         # Local workflow environment set therein.
+        # Allow -S and -D to take effect in Cylc VR.
+        # https://github.com/cylc/cylc-flow/issues/5968
+        self.options.rose_template_vars = []
+        self.options.defines = []
         return WorkflowConfig(
             self.workflow,
             self.flow_file,