Integrating GitHub with Your Shopify Store

Managing Shopify themes becomes frustrating once multiple changes, versions, or developers are involved. I wrote this guide after seeing how quickly theme duplication, manual rollbacks, and limited change tracking slow teams down when stores start scaling.

Integrating Shopify with GitHub solves these issues by introducing proper version control, structured collaboration, and safer deployments. This guide explains exactly how and why to connect your Shopify store with GitHub, using a workflow that works for solo developers and teams alike.

Shopify’s native version control is limited when compared to Git-based workflows. GitHub integration enables proper change tracking, structured collaboration, and controlled deployments.

With GitHub connected, developers can work on separate branches, review changes before deployment, and merge updates safely without overwriting each other’s work. This approach significantly reduces errors while improving development speed and code quality. Multiple developers can work on different features or fixes simultaneously, and Git helps merge their changes together without conflicts, one can also ensure code quality before deploying changes to the live store. By following these easy steps, you integrate your Shopify Store with GitHub.

Create a new repository on GitHub 

Create a new GitHub repository to store your Shopify theme files. This repository will act as the single source of truth for all theme changes, allowing full visibility into edits, versions, and deployment history.

Download the the theme file from your store

Shopify allows theme files to be downloaded as a ZIP package. From the Shopify admin panel, navigate to Online Store → Themes, click Actions, and select Download theme file.

Once received via email, extract the ZIP and ensure the original Shopify theme file structure remains unchanged before pushing it to GitHub.

In your Online Store, click on the action icons and Select download the file, this will send a zip file to your mail.

Upload the extracted theme files into your GitHub repository, preserving Shopify’s required directory structure. Maintaining this structure ensures compatibility when syncing the repository back to Shopify.

In Shopify, navigate to Online Store → Themes → Add theme → Connect from GitHub.

Authenticate your GitHub account, choose whether Shopify should access all repositories or selected ones, and install the integration. This step securely links your Shopify store with GitHub.

Click on login to GitHub Next, and choose your account to continue with Shopify-GitHub Integration

After choosing the account, the next step would be to choose whether to give Shopify access to all the repositories or selected repositories only, it’s totally up to your store requirements whether you want to give access to a few selected repositories or all. 

After Selecting repositories, click on the install button. After completion, you will be able to see on the side window your GitHub Account being displayed along with the option of selecting the repository.

Select the repository containing your Shopify theme and choose the branch that represents your production-ready code. Once connected, Shopify automatically syncs changes from this branch to your store.

And now you finally have your Shopify Store Integrated with your GitHub account

On clicking on view logs, one can see recent theme logs

Once connected, a Shopify Bot appears in the GitHub repository. This bot logs all theme-related commits originating from Shopify, offering full transparency into deployment activity and change history.

When multiple developers are involved, each contributor can work on a separate branch. Pull requests allow changes to be reviewed, compared, and merged into the main branch safely.

GitHub automatically detects conflicts and highlights lines requiring manual resolution, preventing accidental overwrites and broken deployments.

Here we can make pull request to merge the branches to the master branch(i.e. the one which is integrated with Shopify)

Based on the changes, GitHub will either automatically merge or in some cases, notify us that there are conflicts that need to be resolved manually. which one can resolve by reviewing the conflicting lines of code and deciding how to reconcile them with the changes in the pull request.

After successful merging, one can see the code that has been implemented now in the master branch itself and automatically reflected in our Shopify theme. This seamless integration between Shopify and GitHub makes theme development and management much more efficient.

The Shopify Bot on GitHub is a useful feature that appears in your repo after integration. Clicking on it allows you to see all the recent changes on your theme:

This bot facilitates the smooth operation of Shopify Git workflows, making it easier to manage your Shopify theme GitHub repository.

FAQs

1. Why should I connect GitHub to Shopify?

GitHub provides proper version control, collaboration, and rollback capabilities that Shopify’s native tools lack.

2. Does Shopify automatically deploy changes from GitHub?

Yes. Any changes merged into the connected branch are automatically reflected in the Shopify theme.

3. Can multiple developers work safely using this setup?

Yes. Branching and pull requests allow multiple developers to work simultaneously without conflicts.

4. Is Shopify GitHub integration secure?

Yes. Shopify uses OAuth permissions, and access can be restricted to selected repositories.

5. Do I still need Shopify CLI if GitHub is connected?

No, GitHub integration can fully replace manual uploads for theme versioning and deployment.

Conclusion

Integrating GitHub with Shopify transforms theme development from a manual, error-prone process into a structured and scalable workflow. Version control, branching, and pull requests make collaboration predictable and safe, even as teams grow.

By following this setup, theme changes remain traceable, deployments become controlled, and development workflows stay efficient without duplicating themes or risking live store stability.