diff --git a/aclocal.m4 b/aclocal.m4
index 7fa79fffa4f..d09d91b7aff 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -231,8 +231,6 @@ wine_fn_has_flag ()
 wine_fn_depend_rules ()
 {
     wine_fn_append_file SUBDIRS $ac_dir
-    wine_fn_append_rule \
-"Makefile: $srcdir/$ac_dir/Makefile.in"
 }
 
 wine_fn_pot_rules ()
diff --git a/configure b/configure
index 7ed69634d32..c11b2663d8d 100755
--- a/configure
+++ b/configure
@@ -7426,8 +7426,6 @@ wine_fn_has_flag ()
 wine_fn_depend_rules ()
 {
     wine_fn_append_file SUBDIRS $ac_dir
-    wine_fn_append_rule \
-"Makefile: $srcdir/$ac_dir/Makefile.in"
 }
 
 wine_fn_pot_rules ()
diff --git a/tools/makedep.c b/tools/makedep.c
index d46c715aff1..e514cb3a17e 100644
--- a/tools/makedep.c
+++ b/tools/makedep.c
@@ -2845,15 +2845,22 @@ static struct strarray output_sources( const struct makefile *make )
 
     if (make->subdirs.count)
     {
+        struct strarray makefile_deps = empty_strarray;
         struct strarray distclean_files = empty_strarray;
+
         for (i = 0; i < make->subdirs.count; i++)
         {
+            strarray_add( &makefile_deps, top_dir_path( make, base_dir_path( make->submakes[i],
+                                                         strmake ( "%s.in", output_makefile_name ))));
             strarray_add( &distclean_files, base_dir_path( make->submakes[i], output_makefile_name ));
             if (!make->src_dir)
                 strarray_add( &distclean_files, base_dir_path( make->submakes[i], ".gitignore" ));
             if (make->submakes[i]->testdll)
                 strarray_add( &distclean_files, base_dir_path( make->submakes[i], "testlist.c" ));
         }
+        output( "Makefile:" );
+        output_filenames( makefile_deps );
+        output( "\n" );
         output( "distclean::\n");
         output( "\trm -f" );
         output_filenames( distclean_files );