How to Safely Upgrade n8n Without Losing Workflows or Data

Upgrading your n8n instance is essential to access new features, security patches, and performance improvements. However, many users are concerned about losing data or facing errors during the update process.

In this guide, you will learn:

• How to safely upgrade n8n using npm
• How to handle the ENOTEMPTY error
• The difference between npm install -g and npm update -g
• How to upgrade when using either PM2 or a system service
• How to ensure your workflows and credentials are preserved

Where n8n Stores Your Data

Before any upgrade, it’s important to understand where your n8n instance stores its data. All important data (including workflows, credentials, and execution history) is saved in the .n8n folder, typically located at:

/home/your-username/.n8n

As long as this folder is not deleted or overwritten, your data will remain intact after the update.

Recommended Step: Backup Your Data

Even though the update process is safe, it’s a good practice to take a backup of the .n8n folder:

cp -r ~/.n8n ~/.n8n-backup-$(date +%Y%m%d)

Step 1: Stop n8n Before Updating

If You’re Using PM2:

pm2 stop n8n

If You’re Using systemd:

sudo systemctl stop n8n

Step 2: Update n8n Using npmThere are two commands people often consider:Option A: Use npm install -g (Recommended)

This will always fetch the latest version from the registry:

sudo npm install -g n8n --unsafe-perm=true

Option B: Use npm update -g (Not Always Reliable)

This attempts to update globally installed packages only if they’re outdated according to the lockfile, but may not work consistently for CLI tools like n8n.

sudo npm update -g n8n

Recommendation: Always prefer npm install -g n8n for version upgrades to ensure it pulls the latest.

Step 3: Handle Common Installation Errors

Problem: ENOTEMPTY Error

You might encounter the following error:

npm ERR! ENOTEMPTY: directory not empty, rename '/usr/lib/node_modules/n8n' -> '/usr/lib/node_modules/.n8n-xxxx'

Cause: A previous install left behind a temporary or partial folder.

Solution:

1. Delete the temporary directory:

sudo rm -rf /usr/lib/node_modules/.n8n-*

2. Retry the installation:

sudo npm install -g n8n --unsafe-perm=true

3. If permission issues persist, you may run:

sudo chown -R $(whoami) /usr/lib/node_modules

Or:

sudo npm install -g n8n --unsafe-perm=true --force

Step 4: Verify the Installation

Once the install completes:

n8n --version

Confirm the version is updated to the latest release.

Step 5: Restart n8n

If You’re Using PM2:

pm2 restart n8n
pm2 status

If You’re Using systemd:

sudo systemctl start n8n
sudo systemctl status n8n

Optional: Auto-Start on Boot

To ensure n8n starts automatically on reboot:

For PM2:

pm2 startup
pm2 save

For systemd:

sudo systemctl enable n8n

Summary: Best Practices for Updating n8n

• Always stop the running instance before upgrading.
• Prefer npm install -g n8n --unsafe-perm=true over npm update.
• Back up your .n8n directory before making any changes.
• Resolve any ENOTEMPTY errors by removing .n8n-* temp directories.
• Use the appropriate restart method depending on your deployment type.

Final Thoughts

Updating n8n is straightforward and safe when done properly. By understanding where your data is stored and following the proper update procedure, you can ensure that your automation workflows remain secure and uninterrupted.

Would you like an automation script to handle updates weekly or monthly? Or need help migrating to Docker or a cloud deployment? Get in touch and we’ll help optimize your setup.