Two GitHub accounts, one computer · step 5 of 7

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)

The key file name and the “Title” label on GitHub are arbitrary. What must match exactly is the public key contents and which account you add it to. More in the “How it works” step.

3. Wire the keys into .gitconfig-userX

This is the file you created in step 1 of the tutorial (e.g. ~/.gitconfig-user1). Now you add a [core] section to it pointing at a specific key.

Open the file with the nano terminal editor (if you prefer vim or something else, use that instead):

nano ~/.gitconfig-user1

If the file already exists from step 1 (with a [user] section), you’ll see its content. Move to the end of the file and add the new section. The whole file should look like this:

[user]
    name = User1
    email = user1@example.com
[core]
    sshCommand = "ssh -i ~/.ssh/id_ed25519_user1 -o IdentitiesOnly=yes"

Save and exit nano: Ctrl+O (write out), Enter (confirm the file name), Ctrl+X (exit). Repeat the same for .gitconfig-user2, swapping user1 for user2 in both places (the file name and the key path inside sshCommand).

Alternative without opening an editor — append the section directly from the terminal:

cat >> ~/.gitconfig-user1 << 'EOF'
[core]
    sshCommand = "ssh -i ~/.ssh/id_ed25519_user1 -o IdentitiesOnly=yes"
EOF

This appends the [core] section to the end of the file without touching what’s already there. Verify:

cat ~/.gitconfig-user1

You should see both the [user] and [core] sections, one after the other.

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.