diff --git a/xen/Makefile b/xen/Makefile
index 59d368e4d8..fdf9fd3f22 100644
--- a/xen/Makefile
+++ b/xen/Makefile
@@ -374,6 +374,7 @@ $(KCONFIG_CONFIG): tools_fixdep
 # This exploits the 'multi-target pattern rule' trick.
 # The syncconfig should be executed only once to make all the targets.
 include/config/%.conf include/config/%.conf.cmd: $(KCONFIG_CONFIG)
+	$(Q)rm -f include/config/auto.conf
 	$(Q)$(MAKE) $(build)=tools/kconfig syncconfig
 
 ifeq ($(CONFIG_DEBUG),y)
diff --git a/xen/Rules.mk b/xen/Rules.mk
index 8af3dd7277..d759cccee3 100644
--- a/xen/Rules.mk
+++ b/xen/Rules.mk
@@ -15,7 +15,9 @@ srcdir := $(srctree)/$(src)
 PHONY := __build
 __build:
 
--include $(objtree)/include/config/auto.conf
+ifneq ($(firstword $(subst /, ,$(obj))),tools)
+include $(objtree)/include/config/auto.conf
+endif
 
 include $(XEN_ROOT)/Config.mk
 include $(srctree)/scripts/Kbuild.include