Headscale Backup

headscale-backup

Overview

Headscale state is stored in SQLite (its database), config.yaml, policy.json, and TLS certificates. Regular backups are critical before upgrades, as database corruption or misconfiguration can result in complete loss of node registration and routing state. This skill provides three scripts covering the full lifecycle: backup, restore, and migration.

Backup Contents

A complete backup tarball includes:

• SQLite DB — Full node state, users, routes, pre-auth keys, API keys
• config.yaml — Headscale server configuration
• policy.json — ACL policy file (if present)
• Certs and keys — TLS certificate, private key, and node private key (/var/lib/headscale/)
• DERP map — DERP configuration file (if customized)

Backup Methods

• sqlite3 .backup (recommended) — Safe for live databases; uses SQLite online backup API. This is what hs-backup.sh uses.
• File copy (cp) — Requires stopping headscale first to avoid WAL corruption.

Restore

1. Stop headscale service
2. Restore files from backup tarball
3. Start headscale service
4. Verify with a health check or headscale nodes list

Migration

1. Backup on source host (or use an existing backup)
2. rsync or scp the backup tarball to the target host
3. Set up headscale on the target (same version)
4. Restore from backup on target
5. Update DNS to point to the new server
6. Verify clients reconnect

Version Compatibility

Source and target headscale versions should match exactly. Restoring a database from a different headscale version may cause schema migration failures or data corruption. Check versions with headscale version before migrating.

Automated Backups (Cron)

Set up a daily cron job:

0 2 * * * /path/to/hs-backup.sh --auto --output-dir /backups/headscale/

Gotchas

• SQLite WAL mode: sqlite3 .backup is safe; cp of the database file while headscale is running will produce a corrupt copy.
• Version mismatch: Restoring to a different headscale version may break schema migrations.
• Node keys: If node keys change, all nodes must re-authenticate.
• API keys: API keys are stored hashed in the database; restoring a DB backup does not recover the original key secrets — regenerate them with headscale apikeys create.
• Pre-auth keys: Pre-auth keys are restored along with the database, but if they've expired they won't work.

Environment

• HEADSCALE_URL — Headscale server URL
• HEADSCALE_API_KEY — API key for health checks and validation

Trigger Conditions

• "backup headscale"
• "restore headscale"
• "migrate headscale"
• "headscale backup"

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: magnus919
• Source: magnus919/agent-skills
• License: MIT

Install and usage instructions live in the source repository linked above.