diff --git a/red/nodes/index.js b/red/nodes/index.js
index b29a8a7fb..72fe265f5 100644
--- a/red/nodes/index.js
+++ b/red/nodes/index.js
@@ -129,7 +129,7 @@ module.exports = {
     getNodeConfig: registry.getNodeConfig,
 
     clearRegistry: registry.clear,
-    cleanNodeList: registry.cleanNodeList,
+    cleanModuleList: registry.cleanModuleList,
 
     // Flow handling
     loadFlows: flows.load,
diff --git a/red/nodes/registry.js b/red/nodes/registry.js
index 4aefb39f3..e2e1eb6a0 100644
--- a/red/nodes/registry.js
+++ b/red/nodes/registry.js
@@ -372,13 +372,18 @@ var registry = (function() {
 
         saveNodeList: saveNodeList,
 
-        cleanNodeList: function() {
+        cleanModuleList: function() {
             var removed = false;
             for (var mod in moduleConfigs) {
                 if (moduleConfigs.hasOwnProperty(mod)) {
                     if (moduleConfigs[mod] && !moduleNodes[mod]) {
-                        registry.removeNode(id);
-                        removed = true;
+                        var nodes = moduleConfigs[mod].nodes;
+                        for (var node in nodes) {
+                            if (nodes.hasOwnProperty(node)) {
+                                registry.removeNode(mod+"/"+node);
+                                removed = true;
+                            }
+                        }
                     }
                 }
             }
@@ -775,5 +780,5 @@ module.exports = {
 
     addModule: addModule,
     removeModule: registry.removeModule,
-    cleanNodeList: registry.cleanNodeList
+    cleanModuleList: registry.cleanModuleList
 };
diff --git a/red/server.js b/red/server.js
index 71fd21b76..3952ff71e 100644
--- a/red/server.js
+++ b/red/server.js
@@ -91,7 +91,7 @@ function start() {
                     }
                     if (!settings.autoInstallModules) {
                         util.log("[red] Removing modules from config");
-                        redNodes.cleanNodeList();
+                        redNodes.cleanModuleList();
                     }
                 }
                 defer.resolve();