Back to Blog

GitHub Security Best Practices: Protecting Your Code in 2023

GitHub Security Best Practices: Protecting Your Code in 2023

Introduction

With over 100 million developers and more than 330 million repositories, GitHub has become the world's largest host of source code. As your team's codebase grows, so does the importance of implementing robust security practices. Whether you're an individual developer or part of a large organization, securing your GitHub repositories should be a top priority. In this comprehensive guide, we'll explore essential GitHub security best practices that will help protect your valuable code assets.

Why GitHub Security Matters

Security breaches can lead to devastating consequences, including:

  • Exposure of sensitive code and intellectual property
  • Unauthorized access to private repositories
  • Compromised credentials and authentication tokens
  • Supply chain attacks affecting downstream dependencies
  • Damage to your organization's reputation

Implementing proper security measures isn't just an option—it's a necessity for responsible development.

Essential GitHub Security Best Practices

1. Enable Two-Factor Authentication (2FA)

Two-factor authentication is your first line of defense against unauthorized access. GitHub supports multiple 2FA methods:

  • SMS text messages
  • TOTP (Time-based One-Time Password) applications like Authy or Google Authenticator
  • Security keys (FIDO U2F) such as YubiKey

Pro tip: Security keys provide the strongest protection against phishing attacks. If your organization can afford them, they're worth the investment.

# Enable 2FA in GitHub:
Settings > Password and authentication > Two-factor authentication > Enable

2. Implement Branch Protection Rules

Branch protection rules prevent force pushes, ensure code reviews, and enforce status checks before merging changes. This is crucial for maintaining code quality and security.

Key branch protection settings include:

  • Requiring pull request reviews before merging
  • Requiring status checks to pass before merging
  • Requiring signed commits
  • Restricting who can push to matching branches

These settings can be configured in your repository's settings under "Branches."

3. Use GitHub's Security Features

GitHub provides several built-in security tools:

Dependabot Alerts and Security Updates

Dependabot automatically identifies vulnerabilities in your dependencies and creates pull requests to update them to the latest secure version.

# Enable Dependabot alerts:
Repository > Settings > Security & analysis > Enable Dependabot alerts

Code Scanning with CodeQL

GitHub's code scanning feature uses CodeQL to analyze your code for potential security vulnerabilities and coding errors. It supports multiple languages including JavaScript, TypeScript, Python, Java, and Go.

# Enable code scanning:
Repository > Settings > Security & analysis > Enable code scanning

Secret Scanning

This feature scans your repositories for known types of secrets (API keys, authentication tokens, etc.) to prevent fraudulent use of accidentally committed credentials.

# Enable secret scanning:
Repository > Settings > Security & analysis > Enable secret scanning

4. Manage Access Carefully

Practice the principle of least privilege by:

  • Regularly reviewing organization members and their permissions
  • Using fine-grained access controls to limit repository access
  • Creating teams with specific sets of permissions
  • Removing inactive users promptly
  • Using outside collaborators instead of full members when possible

5. Conduct Regular Security Audits

Regularly audit your GitHub organization for:

  • Stale repositories that are no longer maintained
  • Unused or excessive permissions
  • Exposed secrets or credentials
  • Outdated dependencies
  • Inactive user accounts

GitHub's audit log (available to organization owners) provides detailed information about activities within your organization.

6. Sign Your Commits

Signed commits verify that commits come from a trusted source. By signing your commits with GPG or S/MIME, you add an extra layer of verification that the code changes were actually made by you.

# Configure Git to sign commits
git config --global user.signingkey YOUR_GPG_KEY_ID
git config --global commit.gpgsign true

# To create a signed commit
git commit -S -m "Your commit message"

7. Implement a Security Policy

Create a SECURITY.md file in your repository to:

  • Define your security policy
  • Provide instructions for reporting vulnerabilities
  • Explain your disclosure policy
  • Set expectations for response times

This helps security researchers responsibly disclose vulnerabilities they may discover in your code.

8. Use GitHub Actions Securely

GitHub Actions allow you to automate workflows, but they can also introduce security risks if not properly configured:

  • Limit permissions for GitHub tokens
  • Pin actions to a specific SHA (not just a tag or branch)
  • Use secrets for sensitive information
  • Audit third-party actions before using them
  • Consider using GitHub's allowlist to restrict which actions can be used
# Example of limiting token permissions in GitHub Actions
permissions:
  contents: read
  issues: write

9. Implement Repository Templates

For organizations that create many repositories with similar structures, using repository templates ensures that security configurations are consistently applied across all new projects.

10. Monitor and Respond to Security Alerts

Set up monitoring for security alerts and establish a process for:

  • Triaging security alerts
  • Assigning responsibility for remediation
  • Setting SLAs for addressing critical vulnerabilities
  • Tracking metrics on response times and resolution rates

Advanced GitHub Security Considerations

Supply Chain Security

Modern applications often depend on dozens or even hundreds of open-source packages. To secure your supply chain:

  • Implement a dependency review process
  • Consider using GitHub's Dependency Review API
  • Keep an updated Software Bill of Materials (SBOM)
  • Use dependency locking (package-lock.json, Gemfile.lock, etc.)

Integration with Security Tools

GitHub can be integrated with external security tools to enhance your security posture:

  • SAST (Static Application Security Testing) tools
  • Container security scanning
  • Compliance scanning
  • Vulnerability management platforms

Security for GitHub Enterprise

If you're using GitHub Enterprise, additional security measures include:

  • SAML single sign-on
  • LDAP integration
  • CAS integration
  • IP allow lists
  • Audit logging
  • Custom patterns for secret scanning

Conclusion

Implementing robust security practices for your GitHub repositories is not a one-time task but an ongoing commitment. By following the best practices outlined in this guide, you can significantly reduce the risk of security incidents and protect your valuable code assets.

Remember that security is a shared responsibility. Whether you're a developer, repository maintainer, or organization owner, everyone has a role to play in keeping GitHub repositories secure.

Start implementing these security measures today, and make security an integral part of your development workflow. Your future self—and your users—will thank you.

Frequently Asked Questions

How often should I review my GitHub security settings?

It's recommended to review organization-wide security settings quarterly and repository-specific settings whenever there are significant changes to the project or team.

What should I do if I accidentally commit a secret to GitHub?

First, invalidate the secret immediately. Then, remove it from your repository history using tools like BFG Repo-Cleaner or git-filter-branch.

Can I enforce 2FA for all members of my organization?

Yes, organization owners can require all members to enable two-factor authentication from the organization's security settings.

How do I keep dependencies up-to-date without breaking changes?

Use Dependabot's version updates feature to automatically create pull requests when new versions of your dependencies are released, then test these updates in a staging environment before merging.

What's the difference between Dependabot alerts and security updates?

Dependabot alerts notify you about vulnerabilities in your dependencies, while security updates automatically create pull requests to update vulnerable dependencies to the minimum version that resolves the vulnerability.