We bought a pre-built Shopify theme for our first project, thinking it would save us time, and for the most part it did. But midway through customization, one of our developers hit a bug buried in the theme itself. It wasn’t our code or a configuration issue, just something broken in the product we paid for. After a few hours of digging, we gave up and opened a support ticket. That project was our first lesson in something we’ve learned over and over since: the hardest parts of Shopify development aren’t the code. They’re the workflows, the collaboration, and the things you don’t control.

The Collaboration Problem

Version control on Shopify themes is a headache. Multiple developers working on the same files means merge conflicts are constant. The theme architecture, with its Liquid templates, JSON settings, and interconnected snippets, means even small changes can touch several files at once.

But here’s the real issue: Shopify lets people edit themes directly through the admin panel. So while your team is working locally, a client might be in the visual editor rearranging sections or tweaking settings. If you’re not pulling frequently, you’ll overwrite their changes or they’ll overwrite yours. This is why we sync before starting any new work and set clear expectations with clients about when they can safely make edits.

If you’re not already using Shopify CLI for local development, it’s worth the setup. It handles syncing and makes it easier to catch conflicts before they become problems.

Theme Updates Can Wipe Your Work

This one catches a lot of developers off guard. When a theme gets updated, Shopify’s system replaces all theme files. Any custom code you’ve written gets overwritten if it conflicts with the update. Free themes like Dawn use automatic updates that only preserve unmodified files. Paid themes often have more sophisticated migration tools, but it’s still not seamless.

The practical takeaway: always duplicate your theme before updates, document every custom modification, and use clear naming conventions for custom files so you can identify what needs to be reapplied after an update. Some teams maintain a separate Git repository for their customizations to make this easier.

Evaluate the Theme Before You Commit

This one seems obvious, but it’s easy to skip when you’re eager to start building. Before you buy a theme, actually dig into whether it meets the client’s requirements. Run it through Google Lighthouse. Test the responsive layouts thoroughly, including tablets (everyone forgets tablets). Read the reviews, check the documentation, spin up a test store if you can.

Skipping this step is how you end up installing five plugins and writing custom workarounds for features you assumed would just work.

It’s also worth considering whether you need a paid theme at all. Shopify’s free Dawn theme follows Online Store 2.0 best practices and gives you a clean foundation without the risks of third-party code. If your customization needs are significant, starting from Dawn and building up can be more predictable than buying a feature-rich theme and stripping it down.

The Bottom Line

Shopify’s strength is that it’s approachable. Anyone can spin up a store, pick a theme, and start selling. But that approachability creates friction for developers. You’re working in an environment where non-technical users have real power to change things, where version control isn’t straightforward, and where the code you’re building on might have its own hidden issues.

None of this is insurmountable. It just requires going in with your eyes open.