diff --git a/common/xbps-src/shutils/chroot.sh b/common/xbps-src/shutils/chroot.sh
index 3fc144db2d0..c4297bcfa85 100644
--- a/common/xbps-src/shutils/chroot.sh
+++ b/common/xbps-src/shutils/chroot.sh
@@ -127,7 +127,7 @@ chroot_prepare() {
     cp -f $XBPS_SRCPKGDIR/base-files/files/hosts $XBPS_MASTERDIR/etc
 
     mkdir -p $XBPS_MASTERDIR/etc/xbps.d
-    echo "syslog=false" >> $XBPS_MASTERDIR/etc/xbps.d/xbps.conf
+    echo "syslog=false" >> $XBPS_MASTERDIR/etc/xbps.d/00-xbps-src.conf
 
     # Prepare default locale: en_US.UTF-8.
     if [ -s ${XBPS_MASTERDIR}/etc/default/libc-locales ]; then
@@ -153,7 +153,7 @@ chroot_handler() {
     fi
 
     case "$action" in
-        fetch|extract|patch|configure|build|check|install|pkg|bootstrap-update|chroot)
+        fetch|extract|patch|configure|build|check|install|pkg|bootstrap-update|chroot|clean)
             chroot_prepare || return $?
             chroot_init || return $?
             ;;
@@ -191,7 +191,13 @@ chroot_sync_repodata() {
     crossconfdir=$XBPS_MASTERDIR/$XBPS_CROSS_BASE/etc/xbps.d
 
     [ -d $confdir ] && rm -rf $confdir
+    [ -d $crossconfdir ] && rm -rf $crossconfdir
 
+    if [ -d $XBPS_DISTDIR/etc/xbps.d/custom ]; then
+        mkdir -p $confdir $crossconfdir
+        cp -f $XBPS_DISTDIR/etc/xbps.d/custom/*.conf $confdir
+        cp -f $XBPS_DISTDIR/etc/xbps.d/custom/*.conf $crossconfdir
+    fi
     if [ "$CHROOT_READY" ]; then
         hostdir=/host
     else
@@ -296,7 +302,7 @@ chroot_sync_repodata() {
 
     # Make sure to sync index for remote repositories.
     msg_normal "xbps-src: updating repositories for host ($XBPS_MACHINE)...\n"
-    xbps-install -r $XBPS_MASTERDIR -S
+    $XBPS_INSTALL_CMD $XBPS_INSTALL_ARGS -S
 
     if [ -n "$XBPS_CROSS_BUILD" ]; then
         # Copy host keys to the target rootdir.
@@ -306,7 +312,7 @@ chroot_sync_repodata() {
         # Make sure to sync index for remote repositories.
         msg_normal "xbps-src: updating repositories for target ($XBPS_TARGET_MACHINE)...\n"
         env -- XBPS_TARGET_ARCH=$XBPS_TARGET_MACHINE \
-            xbps-install -r $XBPS_MASTERDIR/$XBPS_CROSS_BASE -S
+            $XBPS_INSTALL_CMD $XBPS_INSTALL_ARGS -r $XBPS_MASTERDIR/$XBPS_CROSS_BASE -S
     fi
 
     return 0