diff --git a/Makefile b/Makefile
index 8da3a306d0c0..48990899db0d 100644
--- a/Makefile
+++ b/Makefile
@@ -332,9 +332,7 @@ KALLSYMS	= scripts/kallsyms
 PERL		= perl
 CHECK		= sparse
 
-NOSTDINC_FLAGS  = -nostdinc -isystem $(shell $(CC) -print-file-name=include)
 CHECKFLAGS     := -D__linux__ -Dlinux -D__STDC__ -Dunix -D__unix__
-CHECKFLAGS     += $(NOSTDINC_FLAGS)
 MODFLAGS	= -DMODULE
 CFLAGS_MODULE   = $(MODFLAGS)
 AFLAGS_MODULE   = $(MODFLAGS)
@@ -531,6 +529,10 @@ endif
 
 include $(srctree)/arch/$(ARCH)/Makefile
 
+# arch Makefile may override CC so keep this after arch Makefile is included
+NOSTDINC_FLAGS := -nostdinc -isystem $(shell $(CC) -print-file-name=include)
+CHECKFLAGS     += $(NOSTDINC_FLAGS)
+
 # warn about C99 declaration after statement
 CFLAGS += $(call cc-option,-Wdeclaration-after-statement,)