diff --git a/xbps-src b/xbps-src
index eeec4cac43..f47ae88cdd 100755
--- a/xbps-src
+++ b/xbps-src
@@ -298,6 +298,9 @@ bootstrap_update() {
         return
     fi
     remove_pkg_autodeps
+    msg_normal "xbps-src: cleaning up masterdir...\n"
+    rm -rf $XBPS_MASTERDIR/builddir $XBPS_MASTERDIR/destdir
+    msg_normal "xbps-src: updating $XBPS_MASTERDIR ...\n"
     ${XBPS_INSTALL_CMD} -yu
     return $?
 }