diff --git a/enc/make_encmake.rb b/enc/make_encmake.rb
index a0bf4be969d7e0..09e19f65514499 100755
--- a/enc/make_encmake.rb
+++ b/enc/make_encmake.rb
@@ -129,7 +129,12 @@ def target_transcoders
   dep = ""
 end
 mkin = File.read(File.join($srcdir, "Makefile.in"))
-mkin.gsub!(/@(#{CONFIG.keys.join('|')})@/) {CONFIG[$1]}
+# Variables that should not be expanded in Makefile.in to allow
+# overriding inherited variables at make-time.
+not_expand_vars = %w(CFLAGS)
+mkin.gsub!(/@(#{RbConfig::CONFIG.keys.join('|')})@/) do
+  not_expand_vars.include?($1) ? CONFIG[$1] : RbConfig::CONFIG[$1]
+end
 File.open(ARGV[0], 'wb') {|f|
   f.puts mkin, dep
 }