diff --git a/bootstrap.conf b/bootstrap.conf
index 2b66bc42d..c2f74f406 100644
--- a/bootstrap.conf
+++ b/bootstrap.conf
@@ -182,7 +182,6 @@ gnulib_modules="
   mountlist
   mpsort
   netinet_in
-  non-recursive-gnulib-prefix-hack
   nproc
   nstrftime
   obstack
@@ -339,7 +338,7 @@ XGETTEXT_OPTIONS=$XGETTEXT_OPTIONS'\\\
 '
 
 gnulib_tool_option_extras="--tests-base=gnulib-tests --with-tests --symlink\
- --makefile-name=gnulib.mk
+ --makefile-name=gnulib.mk --automake-subdir
 "
 
 # Build prerequisites
@@ -373,9 +372,6 @@ bootstrap_post_import_hook ()
     && chmod a-w $tmp-1 $tmp-2 \
     && mv -f $tmp-1 $m4f && mv -f $tmp-2 $mkf)
 
-  # Massage lib/gnulib.mk before using it later in the bootstrapping process.
-  build-aux/prefix-gnulib-mk --lib-name=$gnulib_name lib/$gnulib_mk
-
   # Regenerate src/single-binary.mk
   (mkf=src/single-binary.mk tmp=single-binary.tmp \
     && rm -f $mkf $tmp \