It’s true—migrating your repositories and DevOps processes to GitHub is a key step toward improving collaboration, traceability, and team efficiency.

However, a poorly planned migration can lead to code errors, team conflicts, and even security issues.

While there’s no magic formula for success, at CleverIT we understand that knowing the most common challenges—and how to prevent them—is crucial for planning a smooth and secure transition.

In this article, we explore six frequent challenges when migrating to GitHub, along with best practices to overcome them.

1. Lack of management support

A GitHub migration can fail without leadership buy-in. This often results in limited resources, low priority, and resistance to change among development teams.

Best practices:

• Align GitHub’s benefits with your organization’s strategic objectives.
• Clearly communicate how the migration will enhance team collaboration and security.
• Assign specific owners and resources to oversee and support the migration process.

2. Corruption of commit history

This is a more technical challenge. During migration, historical commits may become corrupted, affecting project traceability and integrity.

What to do:

Use specialized tools to detect issues and decide the best approach for each case.

3. Large or oversized binary files

GitHub imposes limits on file sizes, and repositories containing heavy binaries can cause performance issues or increase storage costs when accumulated in large numbers.

Our recommendation:

• Implement Git LFS (Large File Storage) for handling large files. 
• Review the repository, identify heavy files, and move them to a lower-cost storage solution.

4. Mapping users and permissions in GitHub

Poorly configured permissions during migration can lead to security risks and governance problems.

We suggest:

• Plan your team and role structure within your authentication system (these should align with GitHub roles).
• Use user management and automation tools to assign permissions efficiently.
• Validate access permissions in a test environment before migrating final repositories.

5. Lack of standardization

Inconsistent repository names, unclear branch rules, and disorganized code protection policies can make GitHub management difficult.

To prevent this:

• Define clear naming and branching conventions before migrating.
• Set up branch protection rules, mandatory reviews, and commit policies.
• Document standards for the entire team and ensure compliance.

6. Missing external dependencies and artifacts

If critical dependencies or artifacts are left out during migration, builds and deployments may fail.

Recommended practices:

• Review all artifacts, dependencies, and pipelines before migration.
• Ensure migrated repositories include everything needed for project continuity.
• Run build and deployment tests after migration to confirm functionality.

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Migrating to GitHub is not just a technical task—it requires planning, coordination, and strategic vision. That’s what we always emphasize to our clients.

By understanding these challenges and anticipating them, you can ensure a smoother, safer, and more efficient transition—especially when working with an experienced partner like CleverIT.

Planning for problems before they arise is always the best strategy for a successful GitHub migration.