diff --git a/models/migrations/migrations.go b/models/migrations/migrations.go
index 794074524cdd4..bb72b7f5d3c0f 100644
--- a/models/migrations/migrations.go
+++ b/models/migrations/migrations.go
@@ -190,6 +190,8 @@ var migrations = []Migration{
 	NewMigration("add repository code language statistics", addLanguageStats),
 	// v128 -> v129
 	NewMigration("fix merge base for pull requests", fixMergeBase),
+	// v129 -> v130
+	NewMigration("remove dependencies from deleted repositories", purgeUnusedDependencies),
 }
 
 // Migrate database to current version
diff --git a/models/migrations/v129.go b/models/migrations/v129.go
new file mode 100644
index 0000000000000..26f8ed34325e6
--- /dev/null
+++ b/models/migrations/v129.go
@@ -0,0 +1,18 @@
+// Copyright 2020 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 (
+	"xorm.io/xorm"
+)
+
+func purgeUnusedDependencies(x *xorm.Engine) error {
+
+	if _, err := x.Exec("DELETE FROM issue_dependency WHERE issue_id NOT IN (SELECT id FROM issue)"); err != nil {
+		return err
+	}
+	_, err := x.Exec("DELETE FROM issue_dependency WHERE dependency_id NOT IN (SELECT id FROM issue)")
+	return err
+}