Two GitHub accounts, one computer · step 5 of 6

Linux: SSH keys and the agent

ssh-agent started by your desktop environment, or manually in the shell.

1. Generate two SSH keys

ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519_user1 -C "user1@example.com"
ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519_user2 -C "user2@example.com"

2. Add the public keys to GitHub

cat ~/.ssh/id_ed25519_user1.pub

Copy the output and paste it under Settings → SSH and GPG keys on the user1 account. Repeat for user2. (If you have xclip: xclip -sel clip < ~/.ssh/id_ed25519_user1.pub)

3. Wire the keys into .gitconfig-userX

[core]
    sshCommand = "ssh -i ~/.ssh/id_ed25519_user1 -o IdentitiesOnly=yes"

4. Switch the repository remote to SSH

git remote set-url origin git@github.com:user1/repo-name.git
git remote -v

5. Test the connection

ssh -T -i ~/.ssh/id_ed25519_user1 -o IdentitiesOnly=yes git@github.com

You should see Hi user1! You've successfully authenticated....

6. Skip typing the passphrase on every push

Most desktop distros (GNOME, KDE) start ssh-agent automatically at login and integrate it with the system’s keyring (e.g. GNOME Keyring), so a single ssh-add is enough and the passphrase survives future logins.

Add the keys to the agent:

eval "$(ssh-agent -s)"   # only if the agent isn't already running
ssh-add ~/.ssh/id_ed25519_user1
ssh-add ~/.ssh/id_ed25519_user2

Check:

ssh-add -l

On systems without keyring integration (minimal installs, WSL, headless servers) an ssh-agent started with eval "$(ssh-agent -s)" only lives for the current terminal/shell session. To avoid starting it manually every time, add this to ~/.bashrc or ~/.zshrc:

if [ -z "$SSH_AUTH_SOCK" ]; then
  eval "$(ssh-agent -s)" > /dev/null
  ssh-add ~/.ssh/id_ed25519_user1 2>/dev/null
  ssh-add ~/.ssh/id_ed25519_user2 2>/dev/null
fi

This will still prompt for the passphrase on every fresh system login — that’s expected, unless you drop the passphrase from the key entirely (see the security trade-off note in the Windows guide).

WSL (Windows Subsystem for Linux)

If you’re working inside WSL, remember it’s a separate SSH environment from Windows — keys, ~/.gitconfig, and ssh-agent inside WSL are independent from the ones in PowerShell. Stick to one environment (either WSL or Windows) per repository to avoid mixing keys and configs.