diff --git a/common/xbps-src/shutils/chroot.sh b/common/xbps-src/shutils/chroot.sh
index d3951a395ad..9fcf16562d6 100644
--- a/common/xbps-src/shutils/chroot.sh
+++ b/common/xbps-src/shutils/chroot.sh
@@ -46,17 +46,15 @@ reconfigure_base_chroot() {
 
 update_base_chroot() {
     [ -z "$CHROOT_READY" ] && return
-    [ -z "$XBPS_KEEP_ALL" -a -z "$XBPS_SKIP_DEPS" ] && remove_pkg_autodeps
-    msg_normal "xbps-src: cleaning up $XBPS_MASTERDIR masterdir...\n"
-    [ -z "$XBPS_KEEP_ALL" ] && rm -rf $XBPS_MASTERDIR/builddir $XBPS_MASTERDIR/destdir
     msg_normal "xbps-src: updating software in $XBPS_MASTERDIR masterdir...\n"
     # no need to sync repodata, chroot_sync_repodata() does it for us.
     if $(${XBPS_INSTALL_CMD} ${XBPS_INSTALL_ARGS} -nu|grep -q xbps); then
         ${XBPS_INSTALL_CMD} ${XBPS_INSTALL_ARGS} -yu xbps || msg_error "xbps-src: failed to update xbps!\n"
     fi
     ${XBPS_INSTALL_CMD} ${XBPS_INSTALL_ARGS} -yu || msg_error "xbps-src: failed to update base-chroot!\n"
-    [ -z "$XBPS_KEEP_ALL" -a -z "$XBPS_SKIP_DEPS" ] && remove_pkg_autodeps
     msg_normal "xbps-src: cleaning up $XBPS_MASTERDIR masterdir...\n"
+    [ -z "$XBPS_KEEP_ALL" -a -z "$XBPS_SKIP_DEPS" ] && remove_pkg_autodeps
+    [ -z "$XBPS_KEEP_ALL" ] && rm -rf $XBPS_MASTERDIR/builddir $XBPS_MASTERDIR/destdir
 }
 
 # FIXME: $XBPS_FFLAGS is not set when chroot_init() is run