diff --git a/Makefile b/Makefile
index 590512191..9a8277648 100644
--- a/Makefile
+++ b/Makefile
@@ -360,7 +360,7 @@ scripts/basic/%: scripts_basic ;
 
 # This target generates Kbuild's and Config.in's from *.c files
 PHONY += gen_build_files
-gen_build_files:
+gen_build_files: $(wildcard $(srctree)/*/*.c) $(wildcard $(srctree)/*/*/*.c)
 	$(Q)$(srctree)/scripts/gen_build_files.sh $(srctree) $(objtree)
 
 # bbox: we have helpers in applets/
@@ -509,7 +509,7 @@ include $(srctree)/Makefile.flags
 # with it and forgot to run make oldconfig.
 # If kconfig.d is missing then we are probarly in a cleaned tree so
 # we execute the config step to be sure to catch updated Kconfig files
-include/autoconf.h: .kconfig.d .config | gen_build_files
+include/autoconf.h: .kconfig.d .config $(wildcard $(srctree)/*/*.c) $(wildcard $(srctree)/*/*/*.c) | gen_build_files
 	$(Q)$(MAKE) -f $(srctree)/Makefile silentoldconfig
 
 else