diff --git a/eeschema/eeschema_settings.cpp b/eeschema/eeschema_settings.cpp
index a78fd756e8..3a42db4cc1 100644
--- a/eeschema/eeschema_settings.cpp
+++ b/eeschema/eeschema_settings.cpp
@@ -489,6 +489,8 @@ bool EESCHEMA_SETTINGS::MigrateFromLegacy( wxConfigBase* aCfg )
     migrateLegacyColor( "Color4DWireEx",            LAYER_WIRE );
     migrateLegacyColor( "Color4DWorksheetEx",       LAYER_SCHEMATIC_WORKSHEET );
 
+    Pgm().GetSettingsManager().SaveColorSettings( cs, "schematic" );
+
     // LibEdit settings were stored with eeschema.  If eeschema is the first app to run,
     // we need to migrate the LibEdit settings here
 
diff --git a/gerbview/gerbview_settings.cpp b/gerbview/gerbview_settings.cpp
index 85fda300e1..8d6248c99f 100644
--- a/gerbview/gerbview_settings.cpp
+++ b/gerbview/gerbview_settings.cpp
@@ -26,6 +26,7 @@
 #include <pgm_base.h>
 #include <settings/common_settings.h>
 #include <settings/parameters.h>
+#include <settings/settings_manager.h>
 #include <wx/config.h>
 
 
@@ -113,5 +114,31 @@ bool GERBVIEW_SETTINGS::MigrateFromLegacy( wxConfigBase* aCfg )
         }
     }
 
+    COLOR_SETTINGS* cs = Pgm().GetSettingsManager().GetColorSettings();
+
+    auto migrateLegacyColor = [&] ( const std::string& aKey, int aLayerId ) {
+      wxString str;
+
+      if( aCfg->Read( aKey, &str ) )
+          cs->SetColor( aLayerId, COLOR4D( str ) );
+    };
+
+    migrateLegacyColor( "BackgroundColorEx",       LAYER_GERBVIEW_BACKGROUND );
+    migrateLegacyColor( "DCodeColorEx",            LAYER_DCODES );
+    migrateLegacyColor( "GridColorEx",             LAYER_GERBVIEW_GRID );
+    migrateLegacyColor( "NegativeObjectsColorEx",  LAYER_NEGATIVE_OBJECTS );
+    migrateLegacyColor( "WorksheetColorEx",        LAYER_GERBVIEW_WORKSHEET );
+
+    wxString key;
+
+    for( int i = 0, id = GERBVIEW_LAYER_ID_START;
+         id < GERBER_DRAWLAYERS_COUNT + GERBVIEW_LAYER_ID_START; ++i, ++id )
+    {
+        key.Printf( "ColorLayer%dEx", i );
+        migrateLegacyColor( key, id );
+    }
+
+    Pgm().GetSettingsManager().SaveColorSettings( cs, "gerbview" );
+
     return ret;
 }
diff --git a/pcbnew/footprint_editor_settings.cpp b/pcbnew/footprint_editor_settings.cpp
index b148768dcb..8a2e6f4ee2 100644
--- a/pcbnew/footprint_editor_settings.cpp
+++ b/pcbnew/footprint_editor_settings.cpp
@@ -260,7 +260,7 @@ bool FOOTPRINT_EDITOR_SETTINGS::MigrateFromLegacy( wxConfigBase* aCfg )
     migrateLegacyColor( f + "Color4DViaThruEx",          LAYER_VIA_THROUGH );
     migrateLegacyColor( f + "Color4DWorksheet",          LAYER_WORKSHEET );
 
-    manager.Save( cs );
+    manager.SaveColorSettings( cs, "fpedit" );
 
     return ret;
 }
diff --git a/pcbnew/pcbnew_settings.cpp b/pcbnew/pcbnew_settings.cpp
index 8d77565478..6379be6132 100644
--- a/pcbnew/pcbnew_settings.cpp
+++ b/pcbnew/pcbnew_settings.cpp
@@ -646,6 +646,8 @@ bool PCBNEW_SETTINGS::MigrateFromLegacy( wxConfigBase* aCfg )
     migrateLegacyColor( "Color4DViaThruEx",          LAYER_VIA_THROUGH );
     migrateLegacyColor( "Color4DWorksheet",          LAYER_WORKSHEET );
 
+    Pgm().GetSettingsManager().SaveColorSettings( cs, "board" );
+
     // Footprint editor settings were stored in pcbnew config file.  Migrate them here.
     auto fpedit = Pgm().GetSettingsManager().GetAppSettings<FOOTPRINT_EDITOR_SETTINGS>( false );
     fpedit->MigrateFromLegacy( aCfg );