This article's version history on GitHub

Table of Contents:

  1. How I use my Yubikey & GnuPG
  2. A note on GnuPG versions
  3. A note on Yubikey models
  4. Make a backup
  5. Reset factory pins
  6. Edit your new key
  7. Transfer existing GPG keys
  8. Generate new SSH AUTH key
  9. Using AUTH subkey for SSH
  10. Yubikey 4c & Password Store on Android
  11. Set up FIDO U2F for GitHub
  12. Miscellaneous bits

How I use my Yubikey & GnuPG

I use the Yubikey 4c daily to improve my personal and professional security online. The two use cases for me are:

  1. GnuPG private key store
  2. FIDO U2F authentication

I use GnuPG daily to do the following:

  1. signing git tags
  2. using the AUTH key for secure shell authentication
  3. securely store passwords with pass on macOS and using Password Store on Android

I store three 4096-bit subkeys on my Yubikey:

  1. Signing subkey
  2. Encryption subkey
  3. SSH AUTH subkey

My master signing key is stored securely on paper, in a vault. I rarely use it except to create new subkeys, generate revocation certs, etc. Keeping your master signing key offline is the smart choice.

I rarely encrypt or decrypt messages using GnuPG. My use cases are about authentication and verification. Pass/Password Store both use encryption extensively, but it’s all hidden from the user behind a few simple wrapper commands.

I use the Yubikey model that supports USB Type-C. This is the essential piece that allowed me to use the same 4096-bit subkeys on both my laptop and my smartphone. Prior to this I was forced to use 2048-bit keys on the, now defuct, Sigilance card. This was a big pain because the card and card reader are clunky, and it also forced me to use dedicated 2048-bit keys just for for Pass/Password Store. I still used the 4096-bit keys for Linux kernel maintenance. Now I use only the 4096-bit keys for everything and have revoked the 2048-bit keys.

I use FIDO U2F for the websites, apps and services that support the standard. Sadly, many still do not.

A note on GnuPG versions

I use GnuPG v2.1 (aka Modern) on macOS and Debian. Migrating to this version will make backwards-incompatible changes to your keyring. It also comes with some pleasant changes to the otherwise unpleasant experience of using GnuPG, which is worth it in my opinion. Please do not take the decision to upgrade lightly.

It can be difficult to remove versions 1.x and 2.0 from your system. Dependency creep from other packages installed on your computer may bring them back in. Certain applications may only know how to talk to the older libraries and agents. For instance I had to remove all GnuPG-related features from my favorite mail editor in order to keep it working after upgrading to GnuPG v2.1 Modern. I never use GPG for email and I don’t miss the features.

Mac users that have installed GPGTools will be greeted by a native UI when plugging in their Yubikey. Other UNIX users might just do it all in the terminal via the gpg or gpg2 commands (this is what I use in my examples below). Linux desktop users may edit their cards with a GTK- or KDE-specific interface.

Many of these GUI software suites built on top of GnuPG are incompatible with v2.1 Modern. Buyer beware.

A note on Yubikey models

There are a variety of different Yubico products, differences in firmware and hardware revisions, and lots of different procedures floating around the web.

This guide focuses purely on the new Yubikey 4, which involves a simpler process compared to some of the arcane steps required with the older Yubikey Neo. CCID mode is not set by default on the Neo, so make sure you do that first if you have that model.

Additionally this guide focuses on transferring existing keys to the Yubikey 4. I will create a shiny new AUTH key however, just to illustrate how that works. I’m using the Yubikey 4c, which works on both my Macbook Pro and my Google Pixel smarthphone.

If you have a Neo, or if you want to generate new keys on the card I recommend first reading Richard North’s blog. I also recommend Trammell Hudson’s blog, which generates the keys off the card, and then transfers them.

Many of the things in this blog post are more succintly explained in this Linode article, which I recommend reading as well.

I will interchangeable refer to the Yubikey, the 4c, the card and the key card. They are different names for the same thing: the Yubikey dongle plugged into your USB port.

Make a backup

gpg --export-secret-key --armor YOURKEY > YOURKEY.gpg.armor

Leaving the armor file on-disk is dangerous. It contains your private key, which anyone could use to impersonate you. There are lots of great resources on how to make proper backups of your keys via QR codes, USB drives or CDs.

I’m a fan of printing my secret key paper and storing it in a safe or vault. Don’t forget to generate a revocation certificate. Store this in your safe alongside your private key.

Reset the Factory Pins

The admin and user pins on your Yubikey are set at the factory. They are the same for all consumer-grade Yubico devices. We’ll start by changing them to something secret. While we’re at it we will personalize the key card.

Things can go wrong while editing the card sometimes. Below I describe the process of editing the card fully. Read this first before you start typing commands. The log at the bottom of this section contains the actual commands and expected output. Simply follow along with that log and you should be fine.

In case things do go wrong I have also included steps on how to recover if you accidentally lock yourself out of your own key card. This can be caused by too many attempts to unlock the key card with the wrong pin. Resetting the card can also fix some other weird, anomolous behavior.

The factory admin pin is 12345678. The new admin pin you supply must be at least 8 characters long. After changing the admin pin you should see PIN changed. If not, try again and make sure your new pin is at least 8 characters long.

If you see an error like Error changing the PIN: Conditions of use not satisfied it typically means that your pin was too short and was not saved. Try it again with an appropriate length pin.

The factory user pin is 123456. The new user pin you supply must be at least 6 characters long. After you see PIN changed you can move on to personzliation.

It is possible to lock your key card out from any further changes by trying to enter an incorrect pin too many times. You must reset the card to factory settings and try again. Save the following to a file named reset-card-script:

scd serialno
scd apdu 00 20 00 81 08 40 40 40 40 40 40 40 40
scd apdu 00 20 00 81 08 40 40 40 40 40 40 40 40
scd apdu 00 20 00 81 08 40 40 40 40 40 40 40 40
scd apdu 00 20 00 81 08 40 40 40 40 40 40 40 40
scd apdu 00 20 00 83 08 40 40 40 40 40 40 40 40
scd apdu 00 20 00 83 08 40 40 40 40 40 40 40 40
scd apdu 00 20 00 83 08 40 40 40 40 40 40 40 40
scd apdu 00 20 00 83 08 40 40 40 40 40 40 40 40
scd apdu 00 e6 00 00
scd apdu 00 44 00 00
/echo Card has been successfully reset.

And then run gpg-connect-agent -r reset-card-script. You’ll have done a factory reset on the card and can start over from the top of the log.

Personalization is an optional step. The log below details the most common parameters that users might wish to change.

Now plug in your shiny new Yubikey and follow the output of my session below:

Edit your new key

$ gpg2 --card-edit

Reader ...........: Yubico Yubikey 4 OTP U2F CCID
Version ..........: 2.1
Manufacturer .....: Yubico
Serial number ....: XXXXXXXX
Name of cardholder: [not set]
Language prefs ...: [not set]
Sex ..............: unspecified
URL of public key : [not set]
Login data .......: [not set]
Signature PIN ....: not forced
Key attributes ...: rsa2048 rsa2048 rsa2048
Max. PIN lengths .: 127 127 127
PIN retry counter : 3 0 3
Signature counter : 0
Signature key ....: [none]
Encryption key....: [none]
Authentication key: [none]
General key info..: [none]

gpg/card> admin
Admin commands are allowed

gpg/card> passwd

1 - change PIN
2 - unblock PIN
3 - change Admin PIN
4 - set the Reset Code
Q - quit

Your selection? 3
PIN changed.

1 - change PIN
2 - unblock PIN
3 - change Admin PIN
4 - set the Reset Code
Q - quit

Your selection? 1
PIN changed.

1 - change PIN
2 - unblock PIN
3 - change Admin PIN
4 - set the Reset Code
Q - quit

Your selection? q

gpg/card> name
Cardholder's surname: Turquette
Cardholder's given name: Michael

gpg/card> lang
Language preferences: en

gpg/card> sex
Sex ((M)ale, (F)emale or space): M

gpg/card> url
URL to retrieve public key:

gpg/card> login
Login data (account name): mturquette

gpg/card> quit

Transfer existing GnuPG keys

I will populate all three key slots on the Yubikey 4c with subkeys, not the primary signing key. I keep my primary key offline, on paper, in a vault.

For illustration purposes, this is what it looks like to push a primary key to the Yubikey 4c/card (I don’t do this myself):

$ gpg --edit-key
gpg> toggle
gpg> keytocard
Really move the primary key? (y/N) y
Signature key ....: [none]
Encryption key....: [none]
Authentication key: [none]

Please select where to store the key:
   (1) Signature key
   (3) Authentication key
Your selection? 1

The key command select subkeys. Use this to push subkeys to the Yubikey 4c. Personally, I have created a separate signing subkey, and this is what I use to populate the signing slot on my card. In the example below I move the encryption subkey off of my hard disk and onto the key card:

gpg> key 2

pub  rsa4096/3A8F3B2F5A7C9849
     created: 2012-02-18  expires: never       usage: SC
     trust: ultimate      validity: ultimate
sub  rsa2048/04022B7507176F5D
     created: 2016-06-20  expired: 2017-06-20  usage: S
sub* rsa2048/B92E93D2387E0EF4
     created: 2016-06-20  expired: 2017-06-20  usage: E
gpg> keytocard
Signature key ....: BE4B AF4E CAB0 C33F 9235  20C4 3A8F 3B2F 5A7C 9849
Encryption key....: [none]
Authentication key: [none]

Please select where to store the key:
   (2) Encryption key
Your selection? 2
gpg> key 2

Note the final key 2 command. This deselects this particular subkey. You can repeat this process using different subkey indices for the signing subkey (if you have one) and your AUTH subkey (again, if you have one).

Generate a new SSH AUTH key

If you do not have an AUTH subkey and want to use it for SSH key authentication, then follow the steps on this Yubico page.

A few notes:

  1. Create the AUTH key on-disk, instead of on-card
  2. Then move it using the same steps used in the above section
  3. Disable unwanted subkey capabilities before saving the subkey to disk

The Yubico instructions mention to select the ‘A’ capability for AUTH, but they neglect to point out that some GnuPG versions will also select S (Sign) and E (Encrypt) by default. You might want to toggle those off if you already have subkeys for these functions

Using AUTH subkey for SSH

Now that you have the AUTH subkey on-card, let’s setup SSH to use it.

First, add the following line to some sort of script that is run before SSH can be invoked. In my case I put this in ~/.config/omf/, as I use Oh My Fish to manage stuff for fish, my preferred shell.

## GPG and SSH agent configuration

gpg-connect-agent /bye
export SSH_AUTH_SOCK=(gpgconf --list-dirs agent-ssh-socket)

gpg-agent needs SSH support to be explicitly enabled. Add the following to ~/.gnupg/gpg-agent.conf:


Kill all ssh-agent and gpg-agent instances. Typically opening a new shell instance will kick off the machinery above and you should see your new shiny AUTH key by running:

ssh-add -l
4096 SHA256:osIdSEalN4U4ib8wTqpdu1OWKvNTPzIDSZNi58s6AAs cardno:000605762380 (RSA)

You’ll still need to distribute the public key to your remote machines. Generate it with:

ssh-add -L >> ~/.ssh/authorized_keys

It will be the last RSA key in the file. Distribute that to all of the remote authorized_keys files and you’ll be in business.

If you have not already unlocked your key in gpg-agent then you might see the following:

sign_and_send_pubkey: signing failed: agent refused operation
mturquette@'s password:

Doing some sort of gpg operation (encrypt a file, etc) will prompt you for your passphrase, unlock the key, and then you should be able to SSH without issue. Folks not using GnuPG v2.1 (Modern) might find Keychain useful for solving this issue. For v2.1 I’m still trying to figure out the best way…

Yubikey 4c & Password Store on Android

Recent Android smartphones support USB Type-C ports that are compatible with the Yubikey 4c. This means that both Password Store and OpenKeychain can use the Yubikey 4c as a key card.

Pass relies on OpenKeychain for GnuPG support. For users without a hardware key card OpenKeychain expects them to import their GPG secret key onto the phone. In my opinion this is unsafe and terrible advice. Especically for all the cool kids running around with rooted phones and custom ROMs that they simply trust to not do nefarious things with their personal info…

Note that both projects can be a bit slow about pushing the latest versions of their code to the Google Play Store. I recommend building both from source. That’s out of scope for this post, but both build quite easily using the Android SDK and can be pushed over to your phone with a simple adb install pass.apk.

Once both are installed open the OpenKeychain application and plug in your Yubikey 4c. You’ll need to create an identity and bind the key to it. Success looks like this:

Now you’re ready to use Password Store to share encrypted passwords between your smartphone and all of your computers. I host my pass git on a private Github repository. I suggest you do keep access to the git repo private, because even if others cannot decrypt your passwords they will be able to deduce the websites, services, applications, usernames and any other cleartext information that makes up the structure of your ~/.password_store directory.

My config:

Note that I do not use ssh:// for the protocol, but https://. Why? Because SSH requires you to store you SSH private key on the phone. My goal is to never store private key data on the phone.

The only downside to this approach is that in order to pull the latest passwords from Github, I must first remember to decrypt my Github password, then select Pull from remote and finally paste my password into the field. No big deal and worth the peace of mind.

If you’ve followed along to this point you should have GPG subkeys stored on your Yubikey 4c and you should also be able to share encrypted passwords between your workstations using pass and your Android smartphone using a combination of Password Store and OpenKeychain. Congratulations!

Set up FIDO U2F for GitHub

Github Help covers this pretty well already.

I have had success interchangeably using FIDO U2F and GPG on the same key. No need to kill gpg-agent or ssh-agent or hotplug the device (so far).

This only works in Chromium so far, but hopefully mobile apps will start to adopt it in the future.

Miscellaneous bits

If you use a signing subkey like me, and you prefer to use it for most common signing operations, you might want it to be the default key. Unfortunately GnuPG documentation is simply garbage and you might be surprised to find out that setting default-key mysubkey in gpg.conf doesn’t work! Subkeys require a bang at the end, to denote that they are subkeys. My ~/.gnupg/gpg.conf file:

default-key A23A9C9BC325A4D4!

Similarly for git I prefer to use my signing subkey. My ~/.gitconfig file:


	email =
	name = Michael Turquette
	signingkey = A23A9C9BC325A4D4!

The same syntax can be used from the commandline. In this example we sign the f1 file with my signing subkey:

gpg2 -u A23A9C9BC325A4D4! -s f1