diff --git a/www/core/components/settings/controllers/space-usage.js b/www/core/components/settings/controllers/space-usage.js
index 91ebc074b86..fecd58f4a35 100644
--- a/www/core/components/settings/controllers/space-usage.js
+++ b/www/core/components/settings/controllers/space-usage.js
@@ -23,7 +23,7 @@ angular.module('mm.core.settings')
  * @todo When "mock site" is implemented we should have functions to calculate the site usage and delete its files.
  */
 .controller('mmSettingsSpaceUsageCtrl', function($log, $scope, $mmSitesManager, $mmFS, $q, $mmUtil, $translate,
-            $mmCourse, $mmText) {
+            $mmCourse, $mmText, $mmFilepool) {
     $log = $log.getInstance('mmSettingsSpaceUsageCtrl');
 
     // Convenience function to calculate each site's usage, and the total usage.
@@ -107,6 +107,7 @@ angular.module('mm.core.settings')
                 }).then(function(site) {
                     return site.deleteFolder().then(function() {
                         $mmCourse.clearAllModulesStatus(siteid);
+                        $mmFilepool.clearFilepool(siteid);
                         updateSiteUsage(siteData, 0);
                     }).catch(function(error) {
                         if (error && error.code === FileError.NOT_FOUND_ERR) {
diff --git a/www/core/lib/filepool.js b/www/core/lib/filepool.js
index e0b182e8dbc..873cf84f798 100644
--- a/www/core/lib/filepool.js
+++ b/www/core/lib/filepool.js
@@ -414,6 +414,21 @@ angular.module('mm.core')
         self._processQueue();
     };
 
+    /**
+     * Clears the filepool. Use it only when all the files from a site are deleted.
+     *
+     * @module mm.core
+     * @ngdoc method
+     * @name $mmFilepool#clearFilepool
+     * @param  {String} siteId ID of the site to clear.
+     * @return {Promise}       Promise resolved when the filepool is cleared.
+     */
+    self.clearFilepool = function(siteId) {
+        return getSiteDb(siteId).then(function(db) {
+            return db.removeAll(mmFilepoolStore);
+        });
+    };
+
     /**
      * Returns whether a component has files in the pool.
      *