diff --git a/extras/Projucer/Source/Application/jucer_Application.cpp b/extras/Projucer/Source/Application/jucer_Application.cpp
index 5d5460fdc4..67a157659a 100644
--- a/extras/Projucer/Source/Application/jucer_Application.cpp
+++ b/extras/Projucer/Source/Application/jucer_Application.cpp
@@ -136,12 +136,6 @@ void ProjucerApplication::initialiseBasics()
     ImageCache::setCacheTimeout (30 * 1000);
     icons.reset (new Icons());
     tooltipWindow.setMillisecondsBeforeTipAppears (1200);
-
-    if (isRunningCommandLine)
-    {
-        rescanJUCEPathModules();
-        rescanUserPathModules();
-    }
 }
 
 bool ProjucerApplication::initialiseLogger (const char* filePrefix)
diff --git a/extras/Projucer/Source/Application/jucer_CommandLine.cpp b/extras/Projucer/Source/Application/jucer_CommandLine.cpp
index 9e2b2ec22b..8b0d33d44a 100644
--- a/extras/Projucer/Source/Application/jucer_CommandLine.cpp
+++ b/extras/Projucer/Source/Application/jucer_CommandLine.cpp
@@ -25,9 +25,8 @@
 */
 
 #include "jucer_Headers.h"
-#include "../Project/jucer_Module.h"
+#include "jucer_Application.h"
 #include "../Utility/Helpers/jucer_TranslationHelpers.h"
-#include "../Utility/PIPs/jucer_PIPGenerator.h"
 
 #include "jucer_CommandLine.h"
 
@@ -94,6 +93,9 @@ namespace
         {
             if (project != nullptr)
             {
+                if (! justSaveResources)
+                    rescanModulePathsIfNecessary();
+
                 auto error = justSaveResources ? project->saveResourcesOnly (project->getFile())
                                                : project->saveProject (project->getFile(), true);
 
@@ -104,6 +106,35 @@ namespace
             }
         }
 
+        void rescanModulePathsIfNecessary()
+        {
+            bool scanJUCEPath = false, scanUserPaths = false;
+
+            const auto& modules = project->getEnabledModules();
+
+            for (auto i = modules.getNumModules(); --i >= 0;)
+            {
+                const auto& id = modules.getModuleID (i);
+
+                if (isJUCEModule (id) && ! scanJUCEPath)
+                {
+                    if (modules.shouldUseGlobalPath (id))
+                        scanJUCEPath = true;
+                }
+                else if (! scanUserPaths)
+                {
+                    if (modules.shouldUseGlobalPath (id))
+                        scanUserPaths = true;
+                }
+            }
+
+            if (scanJUCEPath)
+                ProjucerApplication::getApp().rescanJUCEPathModules();
+
+            if (scanUserPaths)
+                ProjucerApplication::getApp().rescanUserPathModules();
+        }
+
         std::unique_ptr<Project> project;
     };