diff --git a/src/builder-manifest.c b/src/builder-manifest.c
index 35057f8e..9c9330f2 100644
--- a/src/builder-manifest.c
+++ b/src/builder-manifest.c
@@ -2367,7 +2367,8 @@ builder_manifest_cleanup (BuilderManifest *self,
 
       if (self->rename_icon ||
           self->desktop_file_name_prefix ||
-          self->desktop_file_name_suffix)
+          self->desktop_file_name_suffix ||
+          self->rename_desktop_file)
         {
           g_autoptr(GFile) applications_dir = g_file_resolve_relative_path (app_root, "share/applications");
           g_autofree char *desktop_basename = g_strdup_printf ("%s.desktop", self->id);
@@ -2452,6 +2453,19 @@ builder_manifest_cleanup (BuilderManifest *self,
                 }
             }
 
+          /* If the desktop file didn't set a custom wmclass it relied on the filename
+             matching the wmclass which is no longer true so lets manually set it back. */
+          if (self->rename_desktop_file
+              && !g_strv_contains ((const char * const*)desktop_keys,
+                                   G_KEY_FILE_DESKTOP_KEY_STARTUP_WM_CLASS))
+            {
+              g_autofree char *old_name = g_strndup (self->rename_desktop_file,
+                                                     strlen (self->rename_desktop_file) - strlen (".desktop"));
+
+              g_key_file_set_string (keyfile, G_KEY_FILE_DESKTOP_GROUP,
+                                     G_KEY_FILE_DESKTOP_KEY_STARTUP_WM_CLASS, old_name);
+            }
+
           g_free (desktop_contents);
           desktop_contents = g_key_file_to_data (keyfile, &desktop_size, error);
           if (desktop_contents == NULL)