--- a/python/mozbuild/mozbuild/backend/tup.py
+++ b/python/mozbuild/mozbuild/backend/tup.py
@@ -36,16 +36,17 @@ class BackendTupfile(object):
         self.objdir = objdir
         self.relobjdir = mozpath.relpath(objdir, topobjdir)
         self.environment = environment
         self.name = mozpath.join(objdir, 'Tupfile')
         self.rules_included = False
         self.shell_exported = False
         self.defines = []
         self.host_defines = []
+        self.delayed_generated_files = []
 
         self.fh = FileAvoidWrite(self.name, capture_diff=True)
         self.fh.write('# THIS FILE WAS AUTOMATICALLY GENERATED. DO NOT EDIT.\n')
         self.fh.write('\n')
 
     def write(self, buf):
         self.fh.write(buf)
 
@@ -145,32 +146,41 @@ class TupOnly(CommonBackend, PartialBack
             skip_files = (
                 'buildid.h',
                 'source-repo.h',
             )
             if any(f in skip_files for f in obj.outputs):
                 # Let the RecursiveMake backend handle these.
                 return False
 
-            self._process_generated_file(backend_file, obj)
+            if 'application.ini.h' in obj.outputs:
+                # application.ini.h is a special case since we need to process
+                # the FINAL_TARGET_PP_FILES for application.ini before running
+                # the GENERATED_FILES script, and tup doesn't handle the rules
+                # out of order.
+                backend_file.delayed_generated_files.append(obj)
+            else:
+                self._process_generated_file(backend_file, obj)
         elif isinstance(obj, Defines):
             self._process_defines(backend_file, obj)
         elif isinstance(obj, HostDefines):
             self._process_defines(backend_file, obj, host=True)
         elif isinstance(obj, FinalTargetPreprocessedFiles):
             self._process_final_target_pp_files(obj, backend_file)
         elif isinstance(obj, ObjdirPreprocessedFiles):
             self._process_final_target_pp_files(obj, backend_file)
 
         return True
 
     def consume_finished(self):
         CommonBackend.consume_finished(self)
 
         for objdir, backend_file in sorted(self._backend_files.items()):
+            for obj in backend_file.delayed_generated_files:
+                self._process_generated_file(backend_file, obj)
             with self._write_file(fh=backend_file):
                 pass
 
         with self._write_file(mozpath.join(self.environment.topobjdir, 'Tuprules.tup')) as fh:
             acdefines = [name for name in self.environment.defines
                 if not name in self.environment.non_global_defines]
             acdefines_flags = ' '.join(['-D%s=%s' % (name,
                 shell_quote(self.environment.defines[name]))
@@ -194,17 +204,16 @@ class TupOnly(CommonBackend, PartialBack
         if not os.path.exists(mozpath.join(self.environment.topsrcdir, ".tup")):
             tup = self.environment.substs.get('TUP', 'tup')
             self._cmd.run_process(cwd=self.environment.topsrcdir, log_name='tup', args=[tup, 'init'])
 
     def _process_generated_file(self, backend_file, obj):
         # TODO: These are directories that don't work in the tup backend
         # yet, because things they depend on aren't built yet.
         skip_directories = (
-            'build', # FinalTargetPreprocessedFiles
             'layout/style/test', # HostSimplePrograms
             'toolkit/library', # libxul.so
         )
         if obj.script and obj.method and obj.relobjdir not in skip_directories:
             backend_file.export_shell()
             cmd = self._py_action('file_generate')
             cmd.extend([
                 obj.script,