diff --git a/xbps-src b/xbps-src
index 0a09cba0ba..486a8c77b1 100755
--- a/xbps-src
+++ b/xbps-src
@@ -289,19 +289,29 @@ install_bbootstrap() {
         msg_error "Failed to install bootstrap packages!\n"
     fi
     # Reconfigure base-files to create dirs/symlinks.
-    if xbps-query -r $XBPS_MASTERDIR base-directories &>/dev/null; then
-        XBPS_ARCH=$XBPS_TARGET_PKG xbps-reconfigure -r $XBPS_MASTERDIR -f base-directories &>/dev/null
-    else
+    if xbps-query -r $XBPS_MASTERDIR base-files &>/dev/null; then
         XBPS_ARCH=$XBPS_TARGET_PKG xbps-reconfigure -r $XBPS_MASTERDIR -f base-files &>/dev/null
     fi
-    # Reconfigure ca-certificates.
-    if xbps-query -r $XBPS_MASTERDIR ca-certificates &>/dev/null; then
-        XBPS_ARCH=$XBPS_TARGET_PKG xbps-reconfigure -r $XBPS_MASTERDIR -f ca-certificates &>/dev/null
-    fi
+
     msg_normal "Installed bootstrap successfully!\n"
     chroot_prepare $XBPS_TARGET_PKG || msg_error "Failed to initialize chroot!\n"
 }
 
+reconfigure_bootstrap_pkgs() {
+    local statefile="$XBPS_MASTERDIR/.xbps_chroot_configured"
+    local pkgs="ca-certificates"
+    [ -z "$IN_CHROOT" -o -e $statefile ] && return 0
+    # Reconfigure ca-certificates.
+    msg_normal "Reconfiguring bootstrap packages...\n"
+    for f in ${pkgs}; do
+        if xbps-query $f &>/dev/null; then
+            xbps-reconfigure -f $f
+        fi
+    done
+    touch -f $statefile
+}
+
+
 bootstrap_update() {
     if [ -z "$CHROOT_READY" ]; then
         return
@@ -317,7 +327,7 @@ bootstrap_update() {
 masterdir_zap() {
     for f in bin boot builddir destdir dev etc home lib lib32 lib64 mnt \
         opt proc root run sbin sys tmp usr var host media xbps \
-        void-packages .xbps_chroot_init; do
+        void-packages .xbps_chroot_init .xbps_chroot_reconfigured; do
         if [ -d "$XBPS_MASTERDIR/$f" ]; then
             echo "Removing directory $XBPS_MASTERDIR/$f ..."
             rm -rf $XBPS_MASTERDIR/$f
@@ -606,6 +616,8 @@ if [ -z "$IN_CHROOT" ]; then
     fi
 fi
 
+reconfigure_bootstrap_pkgs
+
 #
 # Main switch.
 #