diff --git a/rhodecode/config/environment.py b/rhodecode/config/environment.py
--- a/rhodecode/config/environment.py
+++ b/rhodecode/config/environment.py
@@ -87,7 +87,8 @@ def load_environment(global_conf, app_co
     init_model(sa_engine_db1)
 
     repos_path = make_ui('db').configitems('paths')[0][1]
-    repo2db_mapper(ScmModel().repo_scan(repos_path))
+    repo2db_mapper(ScmModel().repo_scan(repos_path),
+                   remove_obsolete=True,)
     set_available_permissions(config)
     config['base_path'] = repos_path
     set_rhodecode_config(config)
diff --git a/rhodecode/lib/utils.py b/rhodecode/lib/utils.py
--- a/rhodecode/lib/utils.py
+++ b/rhodecode/lib/utils.py
@@ -451,13 +451,14 @@ def repo2db_mapper(initial_repo_list, re
     for name, repo in initial_repo_list.items():
         group = map_groups(name)
         db_repo = rm.get_by_repo_name(name)
+        # found repo that is on filesystem not in RhodeCode database
         if not db_repo:
             log.info('repository %s not found creating now' % name)
             added.append(name)
             desc = (repo.description
                     if repo.description != 'unknown'
                     else '%s repository' % name)
-            rm.create_repo(
+            new_repo = rm.create_repo(
                 repo_name=name,
                 repo_type=repo.alias,
                 description=desc,
@@ -465,6 +466,10 @@ def repo2db_mapper(initial_repo_list, re
                 owner=user,
                 just_db=True
             )
+            # we added that repo just now, and make sure it has githook
+            # installed
+            if new_repo.repo_type == 'git':
+                ScmModel().install_git_hook(new_repo.scm_instance)
         elif install_git_hook:
             if db_repo.repo_type == 'git':
                 ScmModel().install_git_hook(db_repo.scm_instance)