Complete Guide: Managing Multiple GitHub Accounts on One System

This comprehensive guide helps developers configure and manage multiple GitHub accounts on the same system, enabling seamless switching between personal, work, and client accounts without authentication conflicts.

Overview

Managing multiple GitHub accounts on a single development machine is a common requirement for modern developers. Whether you're maintaining separate personal and professional identities, working with multiple clients, or contributing to different organizations, proper account management ensures secure access control and maintains clear commit attribution.

This guide provides three distinct approaches to handle multiple GitHub accounts, from basic manual switching to advanced automated configuration. Each method has its own advantages and is suitable for different workflow requirements.

Key Benefits:

• Secure isolation between different GitHub accounts
• Automatic switching based on project directory
• Prevention of accidental commits to wrong repositories
• Streamlined authentication across multiple accounts
• Clear audit trail for commit attribution

Understanding the Challenge

When working with multiple GitHub accounts, developers face several technical challenges:

Authentication Conflicts: Git and SSH typically use default credentials, leading to access denials when switching between accounts. The system may authenticate with the wrong account, resulting in permission errors.

Identity Management: Each commit should be attributed to the correct developer identity. Using the wrong name or email in commits can cause confusion in project history and violate organizational policies.

Repository Access: Different repositories may belong to different accounts or organizations, requiring specific authentication credentials for each context.

Workflow Complexity: Manual switching between accounts is error-prone and time-consuming, especially when working on multiple projects simultaneously.

Security Concerns: Improper configuration can lead to credential leakage or unauthorized access to repositories.

Prerequisites

Before implementing any of the solutions in this guide, ensure you have:

• Git installed (version 2.20 or later recommended)
• SSH client available on your system
• Multiple GitHub accounts with appropriate access permissions
• Command line access with ability to edit configuration files
• Basic understanding of Git workflows and SSH key concepts
• Administrative rights to modify SSH and Git configurations

Step-by-Step Setup

1. Generate SSH Keys for Each Account

# For your primary account (if you don't have one already)
ssh-keygen -t ed25519 -C "[email protected]" -f ~/.ssh/id_ed25519
# For your secondary account
ssh-keygen -t ed25519 -C "[email protected]" -f ~/.ssh/id_ed25519_secondary

Note: When prompted for a passphrase, you can either:

• Leave it empty (press Enter) for convenience
• Set a passphrase for additional security

2. Add SSH Keys to GitHub Accounts

Copy your public keys:

# Primary account public key
cat ~/.ssh/id_ed25519.pub
# Secondary account public key
cat ~/.ssh/id_ed25519_secondary.pub

Add to GitHub:

1. Log into each GitHub account
2. Go to Settings → SSH and GPG keys
3. Click New SSH key
4. Paste the respective public key
5. Give it a descriptive title (e.g., "Work Laptop - Primary Account")

3. Configure SSH Config File

Create or edit ~/.ssh/config

# Edit the SSH config file
nano ~/.ssh/config

Add the following configuration:

# Primary GitHub account (default)
Host github.com
HostName github.com
User git
IdentityFile ~/.ssh/id_ed25519
# Secondary GitHub account
Host github-secondary
HostName github.com
User git
IdentityFile ~/.ssh/id_ed25519_secondary

Important:

• The User must always be git for GitHub
• Replace github-secondary with any alias you prefer (e.g. github-work,github-personal)
• Do NOT add .com to your custom host aliases

4. Set Proper Permissions

chmod 600 ~/.ssh/config
chmod 700 ~/.ssh
chmod 600 ~/.ssh/id_ed25519*

5. Test SSH Connections

# Test primary account
ssh -T [email protected]
# Test secondary account
ssh -T git@github-secondary

Expected output:

Hi username! You've successfully authenticated, but GitHub does not provide shell access.

Usage Examples

Cloning Repositories

# Clone with primary account (default)
git clone [email protected]:username/repo-name.git
# Clone with secondary account
git clone git@github-secondary:username/repo-name.git

Setting Up Existing Repositories

# Check current remote
git remote -v
# Switch to secondary account
git remote set-url origin git@github-secondary:username/repo-name.git
# Verify the change
git remote -v

Configure Git Identity Per Repository

# Set identity for current repository
git config user.name "Your Work Name"
git config user.email "[email protected]"
# Or for personal projects
git config user.name "Your Personal Name"
git config user.email "[email protected]"

Troubleshooting

Common Issues and Solutions

1. "Could not resolve hostname github-secondary"

Problem: Using .com with your SSH alias or SSH config not properly set up.

Solution:

• Use git@github-secondary NOT [email protected] 
• Verify your SSH config file exists and has correct permissions

2. "Permission denied (publickey)"

Problem: SSH key not added to GitHub or wrong key being used.

Solutions:

# Test specific key
ssh -i ~/.ssh/id_ed25519_secondary -T [email protected]
# Add key to SSH agent
ssh-add ~/.ssh/id_ed25519_secondary
# Verify key is added to GitHub account

3. "Push rejected" or "Access denied"

Problem: Repository remote URL doesn't match your SSH configuration.

Solution:

# Check remote URL
git remote -v
# Update remote URL to use correct SSH alias
git remote set-url origin git@github-secondary:username/repo.git

4. Wrong author in commits

Problem: Git using wrong user identity.

Solution:

# Check current identity
git config user.name
git config user.email
# Set correct identity for this repository
git config user.name
"Correct Name"
git config user.email
"[email protected]"

Debug Commands

# Test SSH connection with verbose output
ssh -vT git@github-secondary
# Check which SSH key is being used
ssh-add -l
# Verify SSH config parsing
ssh -F ~/.ssh/config -G github-secondary
# Check Git configuration hierarchy
git config --list --show-origin | grep user

Quick Reference Commands

# Generate SSH key
ssh-keygen -t ed25519 -C "[email protected]" -f ~/.ssh/id_ed25519_name
# Test SSH connection
ssh -T git@github-alias
# Clone with specific account
git clone git@github-alias:username/repo.git
# Set repository identity
git config user.name "Name"
git config user.email "[email protected]"
# Change remote URL
git remote set-url origin git@github-alias:username/repo.git
# Check configuration
git config --list --show-origin | grep user
ssh-add -l
git remote -v

Best Practices

Naming Conventions:

• Use descriptive SSH host aliases: github-work,github-personal
• Use consistent email patterns: [email protected]
• Name SSH keys descriptively: id_ed25519_work,id_ed25519_personal

Security:

• Use strong passphrases for SSH keys in production environments
• Regularly rotate SSH keys (annually)
• Keep separate SSH keys for different purposes
• Never share private keys

Backup and Recovery:

• Backup your SSH keys securely
• Document your SSH config setup
• Keep a record of which public keys are associated with which GitHub accounts