Back Up a VPS to S3 Storage with rclone

Snapshots on the same host are not real backups. Copying data to object storage at another provider gives you an off-site copy. This guide shows how to back up a VPS to S3 storage with rclone, encrypted and automated.

Before you start

A Linux VPS with root or sudo.
An S3-compatible bucket and an access key/secret key limited to that bucket. See object storage explained.
The provider's S3 endpoint URL and region.

Install rclone

sudo apt install -y rclone

Distribution packages can be old; the rclone website also offers an install script and static binaries if you need newer features.

Configure the S3 remote

rclone config

Choose n (new remote), name it s3backup.
Storage type: Amazon S3 Compliant Storage Providers, then pick your provider or Other.
Enter the access key, secret key, region and endpoint.
Accept defaults for the rest and save.

Test: rclone lsd s3backup: lists your buckets.

Add encryption (recommended)

Create a second remote of type crypt named s3crypt pointing to s3backup:my-bucket/vps1, and set a strong password and salt. Store these somewhere safe outside the server: without them backups cannot be restored.

Back up files and databases

Dump databases first, e.g. MySQL/MariaDB:

mysqldump --all-databases --single-transaction | gzip > /var/backups/db-$(date +%F).sql.gz

Then copy data:

rclone sync /var/www s3crypt:www --backup-dir s3crypt:archive/$(date +%F) --transfers 8 --log-file /var/log/rclone.log

rclone copy /var/backups s3crypt:db --max-age 48h

sync mirrors the source; --backup-dir keeps changed or deleted files instead of losing them.

Schedule with cron

Save the commands in /usr/local/bin/backup.sh, make it executable, then add to root's crontab (crontab -e):

30 2 * * * /usr/local/bin/backup.sh

Restore

rclone copy s3crypt:www/site1 /var/www/site1

Test a restore to a temporary folder regularly, not only when disaster strikes.

Troubleshooting

SignatureDoesNotMatch: wrong secret key, region or endpoint.
AccessDenied: the key lacks permission for that bucket or action.
Slow uploads: raise --transfers and check the VPS bandwidth.

Frequently asked questions

Should I use sync or copy?

copy never deletes on the destination; sync mirrors deletions. Combine sync with --backup-dir or bucket versioning.

How do I clean up old backups?

Use bucket lifecycle rules, or rclone delete --min-age 30d on archive paths.

Does this work for cPanel hosting?

MdmHost hosting already includes daily JetBackup backups; see cPanel off-site backups for extra copies.

Next steps

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