diff --git a/scripts/upgrade b/scripts/upgrade
index d3a497c..8f892f3 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -78,8 +78,11 @@ if [ "$upgrade_type" == "UPGRADE_APP" ]
 then
 	ynh_script_progression --message="Upgrading source files..." --weight=6
 
+	# Remove the app directory securely
+	ynh_secure_remove --file="$final_path"
+
 	# Download, check integrity, uncompress and patch the source from app.src
-	ynh_setup_source --dest_dir="$final_path" --keep="$final_path/admin/cli/upgrade.php"
+	ynh_setup_source --dest_dir="$final_path"
 fi
 
 chmod 750 "$final_path"