How to Set Up SSH Key Authentication on an Ubuntu Server

ByAkensai

Learning how to set up SSH key authentication on an Ubuntu server is one of the most important security steps you can take as a server administrator. Password-based SSH logins are vulnerable to brute-force attacks. SSH keys replace passwords with cryptographic key pairs, making unauthorized access nearly impossible. In this tutorial, you’ll generate a key pair on your local machine, copy the public key to your Ubuntu server, and configure the SSH daemon to enforce key-only logins. By the end, your server will be significantly more secure. This guide works on Ubuntu 20.04 and 22.04 LTS.

Prerequisites for Setting Up SSH Key Authentication on an Ubuntu Server

Before you start, make sure you have the following in place.

What you need:
– A local machine running Linux, macOS, or Windows (with PowerShell or PuTTY)
– An Ubuntu server (20.04 or 22.04 LTS) with a non-root sudo user
– Existing SSH password access to your server
– Basic familiarity with the Linux terminal

Estimated time: 15–20 minutes

You should already be able to connect to your server via SSH using a password. Don’t disable password authentication until you’ve confirmed your keys work. Locking yourself out is a common mistake. Keep a backup session open while you make configuration changes.

For background reading on SSH key concepts, check out the official Ubuntu OpenSSH Server documentation. It covers the SSH daemon in detail and is worth bookmarking.

Step-by-Step Guide to Setting Up SSH Key Authentication on an Ubuntu Server

Related article: How to Install and Configure Docker on Ubuntu Server 24.04

Follow these steps carefully and in order.

Step 1: Generate an SSH Key Pair on Your Local Machine

Open a terminal on your local computer. Run the following command to generate a 4096-bit RSA key pair:

ssh-keygen -t rsa -b 4096 -C "[email protected]"

You’ll be prompted to choose a save location. Press Enter to accept the default path (~/.ssh/id_rsa). Then set a passphrase. A passphrase adds an extra layer of protection. Don’t skip it.

This creates two files:
– ~/.ssh/id_rsa , your private key (keep this secret)
– ~/.ssh/id_rsa.pub , your public key (this goes on the server)

Step 2: Copy Your Public Key to the Ubuntu Server

Use the ssh-copy-id command to transfer your public key. Replace your_user and your_server_ip with your actual values:

ssh-copy-id your_user@your_server_ip

You’ll be asked for your SSH password one last time. The command automatically appends your public key to ~/.ssh/authorized_keys on the server.

If ssh-copy-id isn’t available (some Windows systems), copy the key manually:

cat ~/.ssh/id_rsa.pub | ssh your_user@your_server_ip "mkdir -p ~/.ssh && cat >> ~/.ssh/authorized_keys"

Step 3: Test Your Key-Based Login

Before changing any server settings, test that the key works:

ssh your_user@your_server_ip

If prompted for your passphrase (not your password), the key is working. Don’t proceed until this step succeeds.

Step 4: Set Correct Permissions on the Server

SSH is strict about file permissions. Wrong permissions will cause authentication to silently fail. Log in to your server and run:

chmod 700 ~/.ssh
chmod 600 ~/.ssh/authorized_keys

These commands restrict access so only your user can read or write those files.

Step 5: Disable Password Authentication on the Server

Now you’ll harden the server by disabling password logins. Open the SSH daemon configuration file:

sudo nano /etc/ssh/sshd_config

Find and update these lines:

PasswordAuthentication no
PubkeyAuthentication yes
AuthorizedKeysFile .ssh/authorized_keys
PermitRootLogin no

Setting PermitRootLogin no prevents direct root SSH access. This is a best practice on any public-facing server.

Step 6: Restart the SSH Service

Apply your changes by restarting the SSH daemon:

sudo systemctl restart ssh

Keep your current session open. Open a new terminal window and try connecting again. If it works, you’re done. If it fails, you can fix the config in your existing session.

Step 7: (Optional) Use an SSH Config File for Convenience

Typing long SSH commands gets old fast. Create a config file on your local machine:

nano ~/.ssh/config

Add an entry like this:

Host myserver
    HostName your_server_ip
    User your_user
    IdentityFile ~/.ssh/id_rsa

Now you can connect by simply typing ssh myserver. This saves time and reduces typos.

Troubleshooting SSH Key Authentication Issues on Ubuntu

Even with careful setup, things can go wrong. Here are the most common problems and how to fix them.

Problem: “Permission denied (publickey)” error

This usually means the server can’t find or read your key. Check these things:

1. Confirm your public key is in ~/.ssh/authorized_keys on the server
2. Run chmod 700 ~/.ssh and chmod 600 ~/.ssh/authorized_keys again
3. Make sure the .ssh directory is owned by your user: ls -la ~/

Problem: SSH still asking for a password after disabling it

Check that you edited the right config file. Some Ubuntu systems have a /etc/ssh/sshd_config.d/ directory with override files. Check for conflicts:

grep -r "PasswordAuthentication" /etc/ssh/

If a file in sshd_config.d/ overrides your setting, edit or remove it.

Problem: Locked out of the server

If you get locked out, most cloud providers (AWS, DigitalOcean, Vultr) offer a web-based console. Use it to re-enable password authentication temporarily. For more detail on recovery options, the OpenSSH manual covers daemon configuration thoroughly.

Warning: Never disable password authentication on a server you can’t access through an alternative method. Always test first.

Problem: Key works locally but not from another machine

Your private key (id_rsa) must exist on every machine you connect from. Generate a new key pair on the second machine and add that public key to authorized_keys as well. One server can hold multiple public keys, one per line.

Conclusion

You’ve now completed the full process of how to set up SSH key authentication on an Ubuntu server. Your server no longer accepts password logins over SSH. That eliminates one of the most common attack vectors for Linux servers. You generated a key pair, transferred the public key, configured the SSH daemon, and tested everything before locking it down.

From here, consider setting up a firewall with ufw to restrict which ports are open. You might also look at fail2ban to block repeated failed login attempts. If you manage multiple servers, an SSH agent can handle your keys automatically without re-entering your passphrase each time. Security is a process, not a one-time setup. Keep your system updated with sudo apt update && sudo apt upgrade regularly.

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