diff --git a/bootstrap.conf b/bootstrap.conf
index 1d8614e7..6b818fc6 100644
--- a/bootstrap.conf
+++ b/bootstrap.conf
@@ -34,7 +34,6 @@ gnulib_modules='
   linked-list
   malloc-gnu
   mbfile mbswidth
-  non-recursive-gnulib-prefix-hack
   obstack
   obstack-printf
   perror progname
@@ -80,13 +79,10 @@ XGETTEXT_OPTIONS_RUNTIME=$XGETTEXT_OPTIONS'\\\
  --keyword=YY_ \\\
 '
 
-gnulib_tool_option_extras='--symlink --conditional-dependencies --makefile-name=gnulib.mk --po-base=gnulib-po --po-domain=bison'
+gnulib_tool_option_extras='--symlink --conditional-dependencies --makefile-name=gnulib.mk --automake-subdir --po-base=gnulib-po --po-domain=bison'
 
 bootstrap_post_import_hook()
 {
-  # Massage lib/gnulib.mk before using it later in the bootstrapping process.
-  build-aux/prefix-gnulib-mk --lib-name="$gnulib_name" "lib/$gnulib_mk"
-
   # Ensure that ChangeLog exists, for automake.
   test -f ChangeLog || touch ChangeLog
 }