diff --git a/models/migrations/migrations.go b/models/migrations/migrations.go
index ae15c9f47..437b63f60 100644
--- a/models/migrations/migrations.go
+++ b/models/migrations/migrations.go
@@ -120,6 +120,8 @@ var migrations = []Migration{
 	NewMigration("give all units to owner teams", giveAllUnitsToOwnerTeams),
 	// v35 -> v36
 	NewMigration("adds comment to an action", addCommentIDToAction),
+	// v36 -> v37
+	NewMigration("regenerate git hooks", regenerateGitHooks36),
 }
 
 // Migrate database to current version
diff --git a/models/migrations/v36.go b/models/migrations/v36.go
new file mode 100644
index 000000000..06f76a26d
--- /dev/null
+++ b/models/migrations/v36.go
@@ -0,0 +1,15 @@
+// Copyright 2017 The Gitea Authors. All rights reserved.
+// Use of this source code is governed by a MIT-style
+// license that can be found in the LICENSE file.
+
+package migrations
+
+import (
+	"code.gitea.io/gitea/models"
+
+	"github.com/go-xorm/xorm"
+)
+
+func regenerateGitHooks36(x *xorm.Engine) (err error) {
+	return models.SyncRepositoryHooks()
+}
diff --git a/models/models.go b/models/models.go
index 6a8fbfe62..1688a6364 100644
--- a/models/models.go
+++ b/models/models.go
@@ -24,7 +24,6 @@ import (
 	// Needed for the MSSSQL driver
 	_ "github.com/denisenkom/go-mssqldb"
 
-	"code.gitea.io/gitea/models/migrations"
 	"code.gitea.io/gitea/modules/log"
 	"code.gitea.io/gitea/modules/setting"
 )
@@ -259,7 +258,7 @@ func SetEngine() (err error) {
 }
 
 // NewEngine initializes a new xorm.Engine
-func NewEngine() (err error) {
+func NewEngine(migrateFunc func(*xorm.Engine) error) (err error) {
 	if err = SetEngine(); err != nil {
 		return err
 	}
@@ -268,7 +267,7 @@ func NewEngine() (err error) {
 		return err
 	}
 
-	if err = migrations.Migrate(x); err != nil {
+	if err = migrateFunc(x); err != nil {
 		return fmt.Errorf("migrate: %v", err)
 	}
 
diff --git a/models/repo.go b/models/repo.go
index 8d9713842..cb6d6d5c3 100644
--- a/models/repo.go
+++ b/models/repo.go
@@ -948,8 +948,12 @@ func cleanUpMigrateGitConfig(configPath string) error {
 // createDelegateHooks creates all the hooks scripts for the repo
 func createDelegateHooks(repoPath string) (err error) {
 	var (
-		hookNames     = []string{"pre-receive", "update", "post-receive"}
-		hookTpl       = fmt.Sprintf("#!/usr/bin/env %s\ndata=$(cat)\nexitcodes=\"\"\nhookname=$(basename $0)\nGIT_DIR=${GIT_DIR:-$(dirname $0)}\n\nfor hook in ${GIT_DIR}/hooks/${hookname}.d/*; do\ntest -x \"${hook}\" || continue\necho \"${data}\" | \"${hook}\"\nexitcodes=\"${exitcodes} $?\"\ndone\n\nfor i in ${exitcodes}; do\n[ ${i} -eq 0 ] || exit ${i}\ndone\n", setting.ScriptType)
+		hookNames = []string{"pre-receive", "update", "post-receive"}
+		hookTpls  = []string{
+			fmt.Sprintf("#!/usr/bin/env %s\ndata=$(cat)\nexitcodes=\"\"\nhookname=$(basename $0)\nGIT_DIR=${GIT_DIR:-$(dirname $0)}\n\nfor hook in ${GIT_DIR}/hooks/${hookname}.d/*; do\ntest -x \"${hook}\" || continue\necho \"${data}\" | \"${hook}\"\nexitcodes=\"${exitcodes} $?\"\ndone\n\nfor i in ${exitcodes}; do\n[ ${i} -eq 0 ] || exit ${i}\ndone\n", setting.ScriptType),
+			fmt.Sprintf("#!/usr/bin/env %s\nexitcodes=\"\"\nhookname=$(basename $0)\nGIT_DIR=${GIT_DIR:-$(dirname $0)}\n\nfor hook in ${GIT_DIR}/hooks/${hookname}.d/*; do\ntest -x \"${hook}\" || continue\n\"${hook}\" $1 $2 $3\nexitcodes=\"${exitcodes} $?\"\ndone\n\nfor i in ${exitcodes}; do\n[ ${i} -eq 0 ] || exit ${i}\ndone\n", setting.ScriptType),
+			fmt.Sprintf("#!/usr/bin/env %s\ndata=$(cat)\nexitcodes=\"\"\nhookname=$(basename $0)\nGIT_DIR=${GIT_DIR:-$(dirname $0)}\n\nfor hook in ${GIT_DIR}/hooks/${hookname}.d/*; do\ntest -x \"${hook}\" || continue\necho \"${data}\" | \"${hook}\"\nexitcodes=\"${exitcodes} $?\"\ndone\n\nfor i in ${exitcodes}; do\n[ ${i} -eq 0 ] || exit ${i}\ndone\n", setting.ScriptType),
+		}
 		giteaHookTpls = []string{
 			fmt.Sprintf("#!/usr/bin/env %s\n\"%s\" hook --config='%s' pre-receive\n", setting.ScriptType, setting.AppPath, setting.CustomConf),
 			fmt.Sprintf("#!/usr/bin/env %s\n\"%s\" hook --config='%s' update $1 $2 $3\n", setting.ScriptType, setting.AppPath, setting.CustomConf),
@@ -968,7 +972,7 @@ func createDelegateHooks(repoPath string) (err error) {
 		}
 
 		// WARNING: This will override all old server-side hooks
-		if err = ioutil.WriteFile(oldHookPath, []byte(hookTpl), 0777); err != nil {
+		if err = ioutil.WriteFile(oldHookPath, []byte(hookTpls[i]), 0777); err != nil {
 			return fmt.Errorf("write old hook file '%s': %v", oldHookPath, err)
 		}
 
diff --git a/routers/init.go b/routers/init.go
index dec7f1818..ad624d3b7 100644
--- a/routers/init.go
+++ b/routers/init.go
@@ -10,6 +10,7 @@ import (
 
 	"code.gitea.io/git"
 	"code.gitea.io/gitea/models"
+	"code.gitea.io/gitea/models/migrations"
 	"code.gitea.io/gitea/modules/cron"
 	"code.gitea.io/gitea/modules/highlight"
 	"code.gitea.io/gitea/modules/indexer"
@@ -50,7 +51,7 @@ func GlobalInit() {
 	if setting.InstallLock {
 		highlight.NewContext()
 		markdown.NewSanitizer()
-		if err := models.NewEngine(); err != nil {
+		if err := models.NewEngine(migrations.Migrate); err != nil {
 			log.Fatal(4, "Failed to initialize ORM engine: %v", err)
 		}
 		models.HasEngine = true