How to Set Up SSH Key-Based Authentication on Ubuntu Server

ByAkensai

Learning how to set up SSH key-based authentication on Ubuntu Server is one of the best things you can do for your server security. Passwords can be guessed, brute-forced, or leaked. SSH keys can’t. They use cryptographic key pairs to verify your identity. This method is far more secure than traditional password login. In this tutorial, you’ll generate an SSH key pair on your local machine, copy the public key to your Ubuntu server, and configure the SSH daemon to enforce key-based login. By the end, you’ll have a server that rejects password authentication entirely. This guide assumes you already have a running Ubuntu server and basic command-line experience.

Estimated time: 15–20 minutes

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Prerequisites for How to Set Up SSH Key-Based Authentication on Ubuntu Server

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

On your local machine:
– A Linux, macOS, or Windows (with WSL or PowerShell) system
– OpenSSH client installed (most systems include this by default)
– Terminal or command-line access

On your Ubuntu server:
– Ubuntu 20.04, 22.04, or 24.04 LTS
– A user account with sudo privileges
– SSH access currently working (password-based is fine for now)
– OpenSSH server installed and running

You can verify OpenSSH is running on your server with this command:

sudo systemctl status ssh

If it’s not installed, run:

sudo apt update
sudo apt install openssh-server -y

You should also know your server’s IP address or hostname. You’ll need it throughout this tutorial. Check the official Ubuntu OpenSSH Server documentation if you need help getting started with basic SSH setup.

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Step-by-Step Guide: How to Set Up SSH Key-Based Authentication on Ubuntu Server

Related article: How to Automate Postgresql Database Backups with Pg_dump and Cron

Follow these steps carefully. Don’t skip ahead , each step builds on the last.

Step 1: Generate an SSH key pair on your local machine

Open a terminal on your local computer and run:

ssh-keygen -t ed25519 -C "[email protected]"

The -t ed25519 flag specifies the key type. Ed25519 is modern and secure. When prompted, choose a save location or press Enter to accept the default (~/.ssh/id_ed25519). Set a passphrase for extra protection. This passphrase encrypts your private key locally.

Step 2: Copy your public key to the Ubuntu server

Use the ssh-copy-id command to transfer your public key:

ssh-copy-id -i ~/.ssh/id_ed25519.pub your_username@your_server_ip

Replace your_username with your actual username and your_server_ip with your server’s IP address. You’ll be prompted for your password one last time. After this step, your public key lives in ~/.ssh/authorized_keys on the server.

If ssh-copy-id isn’t available, copy the key manually:

cat ~/.ssh/id_ed25519.pub | ssh your_username@your_server_ip "mkdir -p ~/.ssh && cat >> ~/.ssh/authorized_keys"

Step 3: Test key-based login

Try logging in before making any configuration changes:

ssh -i ~/.ssh/id_ed25519 your_username@your_server_ip

If you connect without entering your server password, the key is working. Don’t proceed to the next step until this works. Locking yourself out is a real risk if you skip this test.

Step 4: Harden the SSH daemon configuration

Now disable password authentication. Open the SSH config file on your server:

sudo nano /etc/ssh/sshd_config

Find and update these lines:

PasswordAuthentication no
PubkeyAuthentication yes
AuthorizedKeysFile .ssh/authorized_keys
PermitRootLogin no

Make sure none of these lines are commented out with a #. Save and close the file with Ctrl+X, then Y, then Enter.

Step 5: Restart the SSH service

Apply your changes by restarting the SSH daemon:

sudo systemctl restart ssh

Step 6: Verify the new configuration

Open a new terminal window (don’t close your current session). Try connecting again:

ssh your_username@your_server_ip

You should connect using your key. If you try to connect with a wrong key or no key, the server should reject you. That’s exactly what you want.

Step 7: Set correct permissions on the server

SSH is strict about file permissions. Set them correctly to avoid authentication failures:

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

Wrong permissions are one of the most common reasons SSH key login fails silently.

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Troubleshooting SSH Key-Based 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 authorized key. Check these things:

– Confirm the public key in ~/.ssh/authorized_keys matches your local public key
– Check file permissions with ls -la ~/.ssh/
– Run SSH in verbose mode to see exactly what’s happening:

ssh -vvv your_username@your_server_ip

The verbose output tells you which key files are being tried and why authentication fails.

Problem: Locked out after disabling password authentication

If you disabled passwords before confirming key login worked, you may be locked out. Use your hosting provider’s console access (like DigitalOcean’s droplet console or AWS EC2 instance connect) to regain access. Re-enable password auth temporarily, fix the key setup, then disable passwords again.

Problem: SSH agent not forwarding keys

If you’re connecting through a jump host or using an agent, make sure your key is loaded:

ssh-add ~/.ssh/id_ed25519

Verify loaded keys with ssh-add -l.

Problem: Multiple keys causing confusion

If you have several keys, specify which one to use:

ssh -i ~/.ssh/id_ed25519 your_username@your_server_ip

You can also configure this permanently in ~/.ssh/config:

Host myserver
    HostName your_server_ip
    User your_username
    IdentityFile ~/.ssh/id_ed25519

For deeper reading on SSH security best practices, check the SSH Academy guide on ssh-keygen.

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Conclusion

You now know how to set up SSH key-based authentication on Ubuntu Server from start to finish. You generated a key pair, transferred the public key, hardened your SSH configuration, and disabled password login. Your server is now significantly more secure against brute-force attacks and credential theft. The next steps worth exploring include setting up a firewall with ufw, configuring fail2ban to block repeated login attempts, and using SSH config files to manage multiple servers easily. If you manage a WordPress site on this server, securing SSH access is the foundation of everything else. Keep your private key safe, back it up securely, and never share it. Good server security starts with controlling exactly who can get in.

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