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Reinstalling a server's operating system safely

A reinstall wipes the disk and gives you a clean OS. How to prepare, run it from the console, and get back in afterwards.

Nikolay DimitrovSep 14, 2026 · 4 min read

Reinstalling (or rebuilding) a Cloud Server gives you a fresh operating system on the same server and plan. It is the quickest way to recover from a compromised or badly broken system, or to switch from one OS to another. It is also irreversible, so it pays to prepare.

What a reinstall does

  • Erases the primary disk. Every file, database, user and configuration on it is destroyed and cannot be recovered.
  • Keeps the server itself: it stays in the same region on the same plan and billing.
  • Resets access. The root password and SSH host keys change.

Before you start

Copy off everything you need

There is no undo. Copy your data somewhere else first. Two common approaches:

# Dump databasesmysqldump --all-databases --single-transaction | gzip > /root/all-databases.sql.gz # Pull files and the dump to your own machinersync -avz [email protected]:/var/www/ ./server-backup/www/rsync -avz [email protected]:/etc/ ./server-backup/etc/rsync -avz [email protected]:/root/all-databases.sql.gz ./server-backup/

For off-site copies you can keep long term, push them to Object Storage with any S3-compatible tool.

Tip: open your backup and check it before you reinstall. Restore a database dump into a local MySQL, or list the archive. A backup you have never restored is a hope, not a backup.

Write down what you configured

Firewall rules, cron jobs, users and installed packages do not survive a reinstall. These commands capture most of it:

ufw status verbose > ~/firewall.txtcrontab -l > ~/crontab.txtapt-mark showmanual > ~/packages.txt

Run the reinstall

  1. In the console, open your server and choose Open Console.
  2. Choose the reinstall option and pick an operating system image, such as Ubuntu 22.04 or 20.04, or Windows Server 2022 or 2019.
  3. Read the confirmation carefully, then confirm. Nothing is erased until you do.

The reinstall takes a few minutes. Wait for the server to show as running again before you try to connect.

Prefer a long-term-support release unless you have a specific reason not to. LTS releases get security updates for far longer.

Get back in

Set a root password

Open the server page and choose Reset root password. The new password is shown once, so save it straight away.

Clear the old host key

Your SSH client remembers the server's previous fingerprint and will refuse to connect, warning that the host identification has changed. That is expected after a reinstall. Remove the old entry:

ssh-keygen -R 203.0.113.10

Then connect and accept the new fingerprint:

ssh [email protected]

Rebuild the basics

apt update && apt upgrade -yhostnamectl set-hostname server1.example.comssh-copy-id [email protected]   # run this from your own machineufw allow OpenSSH && ufw enable

Then restore your data and reapply the configuration you noted down.

If you cannot connect afterwards

  • Connection refused or timed out. The reinstall is still finishing. Give it a few more minutes.
  • "Remote host identification has changed". Run ssh-keygen -R as shown above.
  • Password rejected. Reset the root password again and paste it carefully.
  • Still nothing. Use Open Console to see what the server is doing. See Locked out of your server?.

Next steps

  • Set up key login on the fresh system: SSH keys.
  • Keep data that matters off the server entirely with Managed Databases and Object Storage.
  • Want a clean server next to the old one instead? Deploy a new Cloud Server and move a Floating IP across when it is ready.
Nikolay DimitrovNikolay looks after Infraista's server fleet from our main data centre in Sofia, Bulgaria, and writes about keeping Linux servers healthy.

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