diff --git a/xbps-src/shutils/chroot.sh.in b/xbps-src/shutils/chroot.sh.in
index ae7b784965..87fd5c1437 100644
--- a/xbps-src/shutils/chroot.sh.in
+++ b/xbps-src/shutils/chroot.sh.in
@@ -198,13 +198,15 @@ create_binsh_symlink()
 
 prepare_binpkg_repos()
 {
-	local repo xver
+	local repo xver CONF_FILE
 
 	# Copy xbps-conf.plist for XBPS utils >= 0.9.0.
 	xver=$($XBPS_PKGDB_CMD -V|awk '{print $2}')
 	if [ -n "$xver" ]; then
+		CONF_FILE=$XBPS_MASTERDIR/usr/local/etc/xbps-conf.plist
 		for f in /etc /usr/local/etc; do
-			if [ -f $f/xbps-conf.plist ]; then
+			if [ -f $f/xbps-conf.plist -a \
+			   ! -f $CONF_FILE ]; then
 				cp -f $f/xbps-conf.plist \
 					${XBPS_MASTERDIR}/usr/local/etc
 			fi