diff --git a/xbps-src b/xbps-src
index b494306f58..f72cc7002c 100755
--- a/xbps-src
+++ b/xbps-src
@@ -311,8 +311,8 @@ reconfigure_bootstrap_pkgs() {
     # Reconfigure ca-certificates.
     msg_normal "Reconfiguring bootstrap packages...\n"
     for f in ${pkgs}; do
-        if xbps-query -r $XBPS_MASTERDIR $f &>/dev/null; then
-            xbps-reconfigure -r $XBPS_MASTERDIR -f $f
+        if $XBPS_QUERY_CMD $f &>/dev/null; then
+            $XBPS_RECONFIGURE_CMD -f $f
         fi
     done
     touch -f $statefile