Using a YubiKey for 2FA when Logging in over SSH

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What is Yubikey?

YubiKeys are small USB dongles that you can plug into your computer. They can simulate keyboard input, allowing you to enter One Time Passwords (OTPs) with the press of a button to authenticate with services like Google, Dropbox and GitHub.

YubiKeys can also be used when logging into a remote server. This guide will show you how to configure your Linode so that a YubiKey must be plugged in and tapped in order to log in to your server using ssh. Depending on your needs, you can also configure a password in addition to the YubiKey for an extra level of security.

If you want to work through this guide but don’t have a YubiKey, you can find one at this link. As of this writing, any key that supports ‘Yubico OTP’ will support two-factor SSH authentication.

Before You Begin

  1. Make sure you have a complete and working Linode as per the instructions in the Getting Started guide.

  2. This guide will use sudo wherever possible. Complete the sections of our Securing Your Server to create a standard user account, harden SSH access and remove unnecessary network services.

  3. Update your local system. Then update your server using the following:

    sudo apt-get update && sudo apt-get upgrade
  4. Test your YubiKey at to make sure it’s working correctly.

Replace each instance of in this guide with your site’s domain name and the appropriate user.

Configure Your YubiKey

If your YubiKey still has its default configuration, you can skip this step. If you’ve made some changes, this section will tell you how to put the appropriate configuration for this guide onto slot 1 of your YubiKey. If you want to use a different slot, make sure you select it instead of slot 1 in the following instructions.

  1. Install the YubiKey Personalization Tool for your system and open it.

  2. Click on the ‘Yubico OTP’ menu in the top-left corner, and select ‘Quick’. Your screen should look like the one below.

  3. Click ‘Write Configuration’. Click ‘Cancel’ on the pop-up window that asks where to save the log file.

    Prompt to save the log file

  4. Now select ‘Upload to Yubico’. In the web form that opens, fill in your email address. Select the field asking for an ‘OTP from the YubiKey’ and touch the button on your YubiKey (or touch and hold if you programmed slot 2). This should fill the field with a string of letters. Complete the captcha and press ‘Upload AES key’.

    AES key upload form

    The page will respond with a table containing your key information. You should keep this data in a safe place. Should you ever lose your YubiKey, you will need this data to reconfigure a new one with the same settings.
  5. Test that your key works by following the instructions for single-factor authentication on If it doesn’t, you may need to wait up to 15 minutes for your key to process on their servers.

Install the Authentication Software

  1. Register for an API key here, by entering your email address and (with the ‘YubiKey one time password’ field selected) touching the button on your YubiKey. Keep the Client ID and Secret Key returned by the website.

    On Ubuntu, you may need to install software-properties-common and python-software-properties to add the repository.
  2. On your Linode, install the pam_yubico package.

    On Ubuntu:

     sudo add-apt-repository ppa:yubico/stable
     sudo apt-get update
     sudo apt-get install libpam-yubico

    On Debian (Wheezy):

     sudo apt-get install libpam-yubico

    On Fedora/EPEL/Arch Linux:

     sudo yum install pam_yubico

    Yubico’s documentation also has instructions on how to build pam_yubico from source.

    You may need to move to wherever PAM modules are stored on your system (usually lib/security). The Ubuntu package will automatically install the module in the appropriate location, but you can check to see whether it’s in the right location with ls /lib/security. It may also be stored in /usr/local/lib/security, in which case you will need to move it manually.
  3. Create the file /etc/ssh/authorized_yubikeys:

     sudo touch /etc/ssh/authorized_yubikeys
  4. Populate this file with the usernames for which you want to enable two-factor authentication and their YubiKey IDs. You can obtain the ID by opening a text editor and touching the button on the YubiKey, and selecting only the first 12 characters. The first line below would be a typical configuration. The subsequent lines show a configuration where users user2, user3, and user4 use multiple YubiKeys and plan to access the server with all of them.

    File: /etc/ssh/authorized_yubikeys
  5. Add auth required id=<client id> key=<secret key> authfile=/etc/ssh/authorized_yubikeys to the start of /etc/pam.d/sshd. Replace <client id> with the ID you retrieved when applying for an API key, and <secret key> with the secret key. If you only want single-factor authentication (either a YubiKey or a password), change required to sufficient to tell the system that a valid YubiKey will be enough to log in.

    File: /etc/pam.d/sshd
    # PAM configuration for the Secure Shell service
    # Add your line below this one
    # v v v v v v
    auth required id=client id key=secret key authfile=/etc/ssh/authorized_yubikeys
    # ^ ^ ^ ^ ^ ^
    # Add your line above this one
    # Standard Un*x authentication.
    @include common-auth
    On some systems, like Arch Linux, you will need to edit /etc/pam.d/system-remote-login instead of /etc/pam.d/sshd.
  6. In /etc/ssh/sshd_config, add or edit the following settings:

    File: /etc/ssh/sshd_config
    ChallengeResponseAuthentication yes
    UsePAM yes

    If you want to only use a YubiKey for single-factor authentication, set PasswordAuthentication no.

  7. Restart the sshd daemon to allow the changes to take effect:

    sudo systemctl restart sshd

Test the YubiKey

Now that this process is done, you can test your login by logging out and back in:


Depending on your setup, you may be prompted for your YubiKey. All you need to do is touch the button; it will enter the key for you. Then, type in your password if you are using multi-factor authentication. It will look something like the image below.

SSH window

You can now log into your server.

Troubleshoot YubiKey

If you encounter any problems, make sure you’ve followed all of the steps in this guide and restarted your server. If these steps don’t solve your issues, you can enable logging, by following these steps:

  1. Add the word debug to the end of the line you added in /etc/pam.d/sshd:

    File: /etc/pam.d/sshd
    auth required id=<client id> key=<secret key> authfile=/etc/ssh/authorized_yubikeys debug
  2. Create a debug log file:

     sudo touch /var/run/pam-debug.log
     sudo chmod go+w /var/run/pam-debug.log
  3. Log data to this file:

     sudo journalctl -f -l
     tail -f /var/run/pam-debug.log
  4. Log in again and analyze this file for clues as to what is causing the problem.

  5. Once you’re done, disable debugging by removing the debug flag from /etc/pam.d/sshd. Then, delete the log file.

More Information

You may wish to consult the following resources for additional information on this topic. While these are provided in the hope that they will be useful, please note that we cannot vouch for the accuracy or timeliness of externally hosted materials.

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