This repo describes my P.I.S. (Policy for Internal Security). You'll find my personal guidelines for SSH / GPG on YubiKey and how to configure and create a key / certificate.

I have several YubiKey, each with different purpose.

Master YubiKey: A YubiKey 5C that keeps Master GPG, SSH CA and root CA for my server. These YubiKey stay in a secure place and will be used only to sign subkey, new SSH Key or new IC.
Keyring YubiKey: A YubiKey 5C NFC on my keyring. This YubiKey is used to keep some passkeys and TOTP for some app. This also contains a GPG subkey and ssh key signed by SSH CA on Master YubiKey.
Laptop YubiKey: A small YubiKey 5 Nano in my laptop that contains a GPG subkey and an ssh key like Keyring YubiKey. This YubiKey Nano stays mostly on my laptop. It slightly increases the security compared to having gpg and ssh directly on my laptop.
Backup YubiKey: A YubiKey 5C, keep in secure place that contains the same passkey and TOTP that the Keyring YubiKey. As security depends on the weakest security measure, some of my apps have passkey enforced or TOTP on YubiKey only. This backup key prevents from losing access in case of losing the Keyring YubiKey.

Install dependencies

sudo dnf install yubikey-manager gnupg pcsc-lite pcsc-tools
sudo systemctl start pcscd
sudo systemctl enable pcscd

GPG

Different types of a GPG key exist:

[C]ertification key (1): Used to sign other keys, this is the Master Key that we want to keep in a secure place.
[S]igning key (10): Used to sign documents, emails, etc.
[E]ncryption key (12): Used to encrypt documents, emails, etc.
[A]uthentication key (11): Used for authentication, for example, for SSH.

I have the strategy below:

Type of key	Validity	Master YK	Keyring YK	Laptop YK
Master [C]	10 Years	Generate in key	-	-
Sign [S]	1Y (renew)	-	unique	unique
Encrypt [E]	10 Years	Generate	clone	clone
Auth [A]	1Y (renew)	-	unique	unique

Master YubiKey

Run GPG on YubiKey, change PIN/Admin/Reset and change a default key

gpg --card-edit
admin
passwd # To change PIN (default: 123456) / Admin code (default: 12345678) / Reset code
key-attr # Change type of key (select ECC 25519 for all keys)

Generate key

generate

Keep aside the revocation file created on your computer

Keyring YubiKey

Create sub-keys

We have to create the subkeys on RAM and move it on the right YubiKey after.

First, connect Master YubiKey on a laptop and edit the key

gpg --expert --edit-key [master_key_id]

Create a 1-year subkey for [S]igning (10) and [A]uthentication (11).

addkey

Save and disconnect YubiKey Master.

Move sub-keys

Connect YubiKey Keyring or YubiKey Laptop.

gpg --edit-key [master_key_id]

Use key N to select the key number N
keytocard
Use key N to deselect the key number N Repeat the operation for Signature and Authentication key

save when everything done

Encryption key

As the encryption key is cloned on several YubiKey, this key needs to be created locally, backup and then copied in all YubiKey.

Create a 10-year subkey for [E]ncryption (12)

addkey
save

Remember to save

Now, export the encryption key

gpg --armor --export-secret-subkeys [master_key_id]> /tmp/backup_keys.asc

Now move the encryption key to the Master YubiKey with keytocard. Once done and save the key is deleted of the local environnement.

Now for each other YubiKey, import the backup key and move it to the YubiKey

gpg --import /tmp/backup_keys.asc
gpg --edit-key [master_key_id]
key N # Select the encryption key
keytocard
save

Remember to securely delete the backup file after.

shred -u /tmp/backup_keys.asc

Export public key

When all subkeys are on the right YubiKey, we can export the public key to share it.

gpg --armor --export [master_key_id] > master-public.asc

This operation has to be done on each renewal of the signing and authentication key, as they are unique on each YubiKey.

SSH

Master YubiKey

I use Yubico authentificator 7.3.0 to change PIN / PUK and Management Key. I also create a certificate in slot 9c of the PIV function with ECCP384 for 10 years (like GPG).

I change PIN for PIV in Yubico authentificator GUI. It's also possible to do it with ykman piv access.

Generate a private key for the CA

Management Key is requested

ykman piv keys generate --algorithm ECCP384 9c public-ca.pem

Generate a self-signed certificate for the CA

PIN is requested

ykman piv certificates generate --subject "CN=SSH CA Klagarge" --valid-days 3650 9c public-ca.pem

Export and add on server

Convert to a standard public key

ssh-keygen -i -m PKCS8 -f public-ca.pem > ssh_ca_master.pub

ssh_ca_master.pub is the public key to put on the server.

For my use case, I want only 1 user with this method, so, I add a line in the ~/.ssh/authorized_keys file of the user with the option cert-authority to allow this CA to sign SSH key for authentication.

cert-authority ecdsa-sha2-nistp384 ...

For global use, you can add the following line in /etc/ssh/sshd_config of the server after copying the public key in /etc/ssh/ssh_ca_master.pub on the server.

TrustedUserCAKeys /etc/ssh/ssh_ca_master.pub

Restart sshd when done with: sudo systemctl restart sshd

Child Keys

Create an SSH key

Disconnect YubiKey Master and connect YubiKey Keyring (or YubiKey Laptop, but commands need to be adapted). Create a key with options

ssh-keygen -t ed25519-sk -O resident -O application=ssh:Klagarge-Keyring -C "YubiKey Keyring" -f ~/.ssh/id_ed25519_sk-keyring

id_ed25519_sk-keyring is the private key that stay on the YubiKey (it's a pointer to the key on the YubiKey)
id_ed25519_sk-keyring.pub is the standard public key that can be shared and used to sign with the CA

Sign it with the CA

Now disconnect YubiKey Keyring and connect YubiKey Master to sign the public key with the CA

ssh-keygen -D /usr/lib64/libykcs11.so.2 \ 
    -s ssh_ca_master.pub \
    -I "Klagarge-Keyring-2026" \
    -n remi,root,Klagarge,her \
    -V +365d \
    ~/.ssh/id_ed25519_sk-keyring.pub

This creates the file id_ed25519_sk-keyring-cert.pub that is the certificate to use for authentication.

Troubleshooting

GPG

Sometimes, for unknown (for me) reason, you need to kill the gpg-agent to be able to use the YubiKey again.

gpgconf --kill gpg-agent

You also sometimes need to restart the pcscd service if the YubiKey is not detected.

sudo systemctl restart pcscd

SSH

If you have an issue with your gpg-agent, you maybe have to wake up the ssh-agent to be able to use the YubiKey again. This basic commande wake up the ssh-agent.

eval $(ssh-agent) # Should response with "Agent pid [number]"

If your key is not found by the ssh agent, you have to manually add the key with:

ssh-add ~/.ssh/id_ed25519_sk-keyring