How to fix /home/user/.ssh/id_rsa already exists. Overwrite (y/n)? in SSH

Before responding to the prompt, consider:

- Keep existing key: If you're using your SSH key with GitHub, GitLab, servers, or other services, overwriting it will break authentication on those services
- Replace key: If the key is old, compromised, or no longer needed, overwriting is safe
- Generate new key with different name: If you need multiple keys (e.g., one for GitHub, one for work servers), create keys with different names

Type n if unsure—you can always generate a new key with a different name later.

At the prompt:

Overwrite (y/n)? n

This preserves your existing SSH key and exits ssh-keygen. If you need additional keys, proceed to the next step.

Use the -f flag to specify a custom path and filename:

ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519_github -C "[email protected]"

Or for RSA:

ssh-keygen -t rsa -b 4096 -f ~/.ssh/id_rsa_work -C "[email protected]"

This creates a new key pair without touching your existing one. You'll be prompted for a passphrase—press Enter twice to skip it, or enter a secure passphrase.

Why this is better: You can maintain multiple SSH keys for different services (GitHub, GitLab, work servers, etc.) without conflicts.

At the prompt:

Overwrite (y/n)? y

Important: Overwriting will replace your existing key. Any services using the old public key will lose access. You'll need to:

1. Copy the new public key:

cat ~/.ssh/id_rsa.pub

2. Update all services that use this key:
- GitHub SSH keys: https://github.com/settings/keys
- GitLab: https://gitlab.com/-/user_settings/ssh_keys
- Servers: Update /home/username/.ssh/authorized_keys
- Cloud platforms: Update SSH key settings

SSH is strict about key file permissions for security. Set them correctly:

chmod 600 ~/.ssh/id_rsa
chmod 644 ~/.ssh/id_rsa.pub
chmod 700 ~/.ssh

- Private key (id_rsa): 600 (read/write for owner only)
- Public key (id_rsa.pub): 644 (readable by all, writable by owner only)
- .ssh directory: 700 (owner can read/write/execute)

If permissions are wrong, SSH will refuse to use the key with "Permissions 0644 for '~/.ssh/id_rsa' are too open." error.

If you're running ssh-keygen in a script and need to auto-confirm the overwrite:

yes | ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519 -N ""

Or with a passphrase:

echo "your_passphrase" | ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519 -N "your_passphrase" -q

Flags:
- -N "": Set empty passphrase (no password prompt)
- -N "passphrase": Set a specific passphrase
- -q: Quiet mode (suppress output)
- yes |: Pipe 'yes' to auto-confirm the overwrite prompt