diff --git a/tools/lisa-buildroot-update-kernel-config b/tools/lisa-buildroot-update-kernel-config
index d98a4105a967b0d172723e520e410f40cde938c3..d77a06d63d7b02d2f5a65befdf76cd7f6d8013b0 100755
--- a/tools/lisa-buildroot-update-kernel-config
+++ b/tools/lisa-buildroot-update-kernel-config
@@ -74,4 +74,6 @@ tee "$fragment" << EOF
 CONFIG_INITRAMFS_SOURCE="$ROOTFS"
 EOF
 
+# merge_config.sh seems to have issue if called from other working directories
+cd "$KERNEL_DIR" &&
 KCONFIG_CONFIG="$KERNEL_CONFIG" "$KERNEL_DIR/scripts/kconfig/merge_config.sh" "$KERNEL_CONFIG" "$fragment"