diff --git a/configure b/configure
index b0a151e2e..8298fc818 100755
--- a/configure
+++ b/configure
@@ -404,10 +404,10 @@ done
 rm -f mk/config.mk.bak
 
 # Environment variables
-[ -n "$CFLAGS" ] && echo "CFLAGS?=$CFLAGS" >> mk/config.mk
-[ -n "$CXXFLAGS" ] && echo "CXXFLAGS?=$CXXFLAGS" >> mk/config.mk
-[ -n "$LDFLAGS" ] && echo "LDFLAGS?=$LDFLAGS" >> mk/config.mk
-[ -n "$DESTDIR" ] && echo "DESTDIR?=$DESTDIR" >> mk/config.mk
+[ -n "$CFLAGS" ] && echo "CFLAGS?=$CFLAGS" > mk/cc.flags.mk
+[ -n "$CXXFLAGS" ] && echo "CXXFLAGS?=$CXXFLAGS" >> mk/cc.flags.mk
+[ -n "$LDFLAGS" ] && echo "LDFLAGS?=$LDFLAGS" >> mk/cc.flags.mk
+[ -n "$DESTDIR" ] && echo "DESTDIR?=$DESTDIR" >> mk/cc.flags.mk
 
 echo "done."
 
diff --git a/mk/spdk.common.mk b/mk/spdk.common.mk
index 10b18e5a0..e3bcc909b 100644
--- a/mk/spdk.common.mk
+++ b/mk/spdk.common.mk
@@ -39,7 +39,7 @@ endif
 endif
 
 include $(SPDK_ROOT_DIR)/mk/config.mk
-
+-include $(SPDK_ROOT_DIR)/mk/cc.flags.mk
 -include $(SPDK_ROOT_DIR)/mk/cc.mk
 
 ifneq ($(V),1)