Overview

This guide walks through installing the GitHub MCP (Model Context Protocol) Server and configuring it for use with Warp AI Agent Mode. The setup supports multiple GitHub accounts running simultaneously, eliminating the need to switch tokens manually.

Prerequisites

  • macOS with Homebrew installed
  • Warp terminal
  • GitHub accounts with Personal Access Tokens
  • GitHub CLI (recommended)

Installation Process

1. Install GitHub MCP Server

Use Homebrew to install the official GitHub MCP Server (Go-based, no Node.js required):

# Install GitHub MCP Server
brew install github-mcp-server

# Verify installation
github-mcp-server --version

Expected output:

GitHub MCP Server
Version: 0.13.0
Commit: Homebrew
Build Date: 2025-08-21T22:20:26Z

2. Generate GitHub Personal Access Tokens

For each GitHub account, create a Personal Access Token with the following scopes:

  • repo (for repository access)
  • issues (for issue management)
  • pull_requests (for PR operations)
  • workflow (for GitHub Actions)

Navigate to: GitHub Settings → Developer settings → Personal access tokens → Tokens (classic)

Configuration

3. Set Up Environment Variables

Add tokens to your shell profile with descriptive names:

# Add to ~/.zshrc
echo '
# GitHub Tokens for MCP Server
export GITHUB_TOKEN_1="ghp_your_first_token_here"
export GITHUB_TOKEN_2="ghp_your_second_token_here"
export GITHUB_PERSONAL_ACCESS_TOKEN="$GITHUB_TOKEN_1"  # Default account
' >> ~/.zshrc

# Reload configuration
source ~/.zshrc

4. Create MCP Configuration File

Create a JSON configuration for dual GitHub account support:

{
  "mcpServers": {
    "github-mcp-1": {
      "command": "github-mcp-server",
      "args": ["stdio"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_your_first_token_here"
      }
    },
    "github-mcp-2": {
      "command": "github-mcp-server",
      "args": ["stdio"],
      "env": {
        "GITHUB_PERSONAL_ACCESS_TOKEN": "ghp_your_second_token_here"
      }
    }
  }
}

Save this as ~/github-mcp-config.json for reference.

Warp AI Integration

5. Configure Warp AI MCP Settings

  1. Open Warp Settings:

    • Press Cmd + , or go to Settings → AI
    • Navigate to MCP Servers section

  2. Add the Configuration: Paste the JSON configuration from step 4 into the MCP servers settings.

  3. Apply Settings: Save the configuration. Warp AI will automatically start both MCP servers.

Verification

6. Test the Setup

Both servers should now be running simultaneously. You can verify by using Warp AI Agent Mode commands:

# Example Agent Mode commands
# "List repositories from the_First account"
# "Show issues in the_Second account repositories"
# "Create a new repository on the_First account"

7. Check Server Status

Verify both servers are accessible:

# Check environment variables (masked output)
echo "Account 1: ${GITHUB_TOKEN_1:0:7}...${GITHUB_TOKEN_1: -4}"
echo "Account 2: ${GITHUB_TOKEN_2:0:7}...${GITHUB_TOKEN_2: -4}"

Features and Capabilities

Dual Account Benefits

  • Simultaneous Access: Both GitHub accounts available without switching
  • Account Isolation: Each server uses its own authentication token
  • Full Read/Write: Both servers configured for complete GitHub API access
  • Persistent Configuration: Survives terminal restarts and system reboots

Available Operations

Through Warp AI Agent Mode, you can perform operations on both accounts:

  • Repository management (create, clone, delete)
  • Issue and PR management
  • File operations (read, create, update)
  • Branch and tag management
  • GitHub Actions workflow management
  • User and organization operations

Troubleshooting

Common Issues

Token Authentication Errors:

# Verify token is set correctly
echo $GITHUB_PERSONAL_ACCESS_TOKEN

# Test token validity
gh auth status

Server Not Starting:

# Check server help
github-mcp-server --help

# Test manual server start
github-mcp-server stdio

Permission Issues:

  • Ensure tokens have appropriate scopes
  • Verify token hasn’t expired
  • Check repository access permissions

Security Considerations

  • Token Storage: Tokens are stored in plain text in shell profiles
  • Access Control: Use tokens with minimal required scopes
  • Token Rotation: Regularly regenerate tokens for security
  • Environment Isolation: Each server runs with isolated authentication

Outcome

This setup provides seamless dual GitHub account integration with Warp AI, enabling efficient multi-account repository management through natural language commands. Both servers run concurrently, eliminating manual token switching and providing full API access to both GitHub accounts.