diff --git a/includes/roots-cleanup.php b/includes/roots-cleanup.php
index b5107d45de..025311c3d6 100644
--- a/includes/roots-cleanup.php
+++ b/includes/roots-cleanup.php
@@ -43,12 +43,13 @@ function roots_clean_plugins($content) {
     return $content;
 }
 
-// only use clean urls if the theme isn't a child
-if ($theme_data['Template'] === '') {
+// only use clean urls if the theme isn't a child or an MU (Network) install
+if ((!defined('WP_ALLOW_MULTISITE') || (defined('WP_ALLOW_MULTISITE') && WP_ALLOW_MULTISITE !== true)) && $theme_data['Template'] === '') {
   add_action('generate_rewrite_rules', 'roots_add_rewrites');
   add_filter('plugins_url', 'roots_clean_plugins');
   add_filter('bloginfo', 'roots_clean_assets');
   add_filter('stylesheet_directory_uri', 'roots_clean_assets');
+  add_filter('template_directory_uri', 'roots_clean_assets');
 }
 
 // redirect /?s to /search/
@@ -73,6 +74,7 @@ function roots_root_relative_url($input) {
 add_filter('bloginfo_url', 'roots_root_relative_url');
 add_filter('theme_root_uri', 'roots_root_relative_url');
 add_filter('stylesheet_directory_uri', 'roots_root_relative_url');
+add_filter('template_directory_uri', 'roots_root_relative_url');
 add_filter('the_permalink', 'roots_root_relative_url');
 add_filter('wp_list_pages', 'roots_root_relative_url');
 add_filter('wp_list_categories', 'roots_root_relative_url');