diff --git a/module/Makefile.in b/module/Makefile.in
index 78e48147ae..d9f73c2878 100644
--- a/module/Makefile.in
+++ b/module/Makefile.in
@@ -24,7 +24,10 @@ modules:
 	$(MAKE) -C @LINUX_OBJ@ SUBDIRS=`pwd` @KERNELMAKE_PARAMS@ $@
 
 clean:
-	$(MAKE) -C @LINUX_OBJ@ SUBDIRS=`pwd` @KERNELMAKE_PARAMS@ $@
+	@# Only cleanup the kernel build directories when CONFIG_KERNEL
+	@# is defined.  This indicates that kernel modules should be built.
+@CONFIG_KERNEL_TRUE@	$(MAKE) -C @LINUX_OBJ@ SUBDIRS=`pwd` @KERNELMAKE_PARAMS@ $@
+
 	if [ -f @SPL_SYMBOLS@ ]; then $(RM) @SPL_SYMBOLS@; fi
 	if [ -f @LINUX_SYMBOLS@ ]; then $(RM) @LINUX_SYMBOLS@; fi
 	if [ -f Module.markers ]; then $(RM) Module.markers; fi