diff --git a/Framework/Core/include/Framework/runDataProcessing.h b/Framework/Core/include/Framework/runDataProcessing.h
index fbf2843d4db01..eee4c4b6583d3 100644
--- a/Framework/Core/include/Framework/runDataProcessing.h
+++ b/Framework/Core/include/Framework/runDataProcessing.h
@@ -197,7 +197,6 @@ int mainNoCatch(int argc, char** argv)
   for (auto& extra : extraOptions) {
     workflowOptions.push_back(extra);
   }
-  workflowOptionsRegistry.loadExtra(extraOptions);
 
   ConfigContext configContext(workflowOptionsRegistry, argc, argv);
   o2::framework::WorkflowSpec specs = defineDataProcessing(configContext);
diff --git a/Framework/Core/src/ConfigParamDiscovery.cxx b/Framework/Core/src/ConfigParamDiscovery.cxx
index 9673f77ed0e42..63c38b7f0ac6c 100644
--- a/Framework/Core/src/ConfigParamDiscovery.cxx
+++ b/Framework/Core/src/ConfigParamDiscovery.cxx
@@ -75,6 +75,7 @@ std::vector<ConfigParamSpec> ConfigParamDiscovery::discover(ConfigParamRegistry&
     for (auto& extra : extras) {
       result.push_back(extra);
     }
+    registry.loadExtra(extras);
   }
   return result;
 }