diff --git a/tools/cli/installers/lib/modules/manager.js b/tools/cli/installers/lib/modules/manager.js
index b4acc3aef..f162593b7 100644
--- a/tools/cli/installers/lib/modules/manager.js
+++ b/tools/cli/installers/lib/modules/manager.js
@@ -734,8 +734,10 @@ class ModuleManager {
         continue;
       }
 
-      // Skip config.yaml templates - we'll generate clean ones with actual values
-      if (file === 'config.yaml' || file.endsWith('/config.yaml')) {
+      // Skip module root config.yaml only - generated by config collector with actual values
+      // Workflow-level config.yaml (e.g. workflows/orchestrate-story/config.yaml) must be copied
+      // for custom modules that use workflow-specific configuration
+      if (file === 'config.yaml') {
         continue;
       }