diff --git a/system/Config.in b/system/Config.in
index 4d070103fd..92712a8e01 100644
--- a/system/Config.in
+++ b/system/Config.in
@@ -92,7 +92,7 @@ config BR2_INIT_SYSTEMD
 	depends on BR2_USE_MMU
 	depends on !BR2_STATIC_LIBS
 	depends on BR2_TOOLCHAIN_HEADERS_AT_LEAST_3_10
-	select BR2_ROOTFS_MERGED_USR
+	select BR2_ROOTFS_MERGED_USR if BR2_ROOTFS_SKELETON_DEFAULT
 	select BR2_PACKAGE_SYSTEMD
 
 comment "systemd needs (e)glibc toolchain, headers >= 3.10"