Hiring an agency to customize your Shopify store is one of the highest-leverage decisions you’ll make for your e-commerce business. Get it right and you end up with a fast, flexible store built on clean code that your team can actually manage. Get it wrong and you’re looking at bloated apps, a crawling storefront, and a codebase so tangled that every future change costs a small fortune.
These ten questions are designed to expose the gap between agencies that know Shopify deeply and those that just know their way around a theme editor.
1. What’s your philosophy on native features versus custom code?
The first thing to ask. It tells you everything you need to know about how they think.
A low-tier shop will reach for custom code or a third-party app the second a feature request lands on their desk. A strong technical agency will first ask what Shopify can already do natively – especially in the context of Online Store 2.0, because now merchants can add sections and blocks to basically any page template without a developer touching it at all.
If they can’t clearly explain when they wouldn’t write custom code, I’d see that as a red flag. Over-engineering is how technical debt is born. The shortcuts and workarounds that accumulate and slow down, increase the costs, and make more fragile every subsequent update or even minor change in the future. Press them on this. Get a specific case, when was the last time they recommended a merchant use a native Shopify feature and didn’t build something custom.
2. How do you manage your development workflow and version control?
This is an easy way to differentiate professional engineering teams from freelancers pretending to be agencies.
Any competent development team uses Git-based version control – GitHub or GitLab are the most common – and deploys through Shopify’s Theme CLI to a staging environment before anything touches the live store. A staging environment is simply a duplicate store where code gets built and tested in isolation. If something breaks there, customers never see it.
What you’re listening for: specific tool names, a clear description of the branching strategy, and a process for code review before deployment. What you’re quietly vetting against: any answer that involves editing code directly in the live theme editor. That’s not a workflow. It’s improvisation with your production store.
Version control also matters when multiple developers are working simultaneously. Without it, one developer’s changes can silently overwrite another’s, and there’s no reliable way to roll back a bad deployment.
3. What’s your QA process for site speed and Core Web Vitals?
Website performance cannot be compromised. For instance, e-commerce websites that load in 1 second have conversion rates 2.5 times higher than those taking 5 seconds to load (Portent). Each custom feature implemented by an agency exerts a site-speed tax on performance if you’re not careful.
Inquire about how an agency plans to prevent performance from dropping post-launch. Following the build, what does the launch process look like? What sort of ongoing maintenance do they offer to ensure security patches don’t degrade site speed? For growing brands that need complex integrations and custom theme builds, partnering with a specialized shopify agency los angeles ensures your development team understands both high-growth retail strategies and the technical nuances of the Shopify Plus ecosystem. Are they available for continuous security support, or would you need to maintain your own staging environment to quickly test and deploy patches?
Nine times out of ten, you’re not going to get maintenance questions at the pitch stage. If you do, they’ll know how to handle the conversation better than sweet-talking you and scooting the question.
4. Can you walk me through your approach to Liquid and custom theme architecture?
Liquid is how Shopify does templating, and how an agency uses it exposes their real engineering depth.
Ask them to explain how they’d structure a custom section. Do they develop reusable schema blocks and allow you to configure the block in a template, or do they hardcode a specific configuration directly into the template file? Ask how they determine naming conventions and file organization within a theme. These are not trick questions – a developer who knows Liquid well will have immediate answers to all of them.
What you’re really vetting for is whether they produce a theme that your internal team (or the next agency you hire) can actually work with. A well-structured Liquid theme with easily understandable schema definitions and logically organized related files is an asset. A badly structured one is a bill you pay every time you want to get some work done for years.
5. How do you handle Checkout Extensibility for Shopify Plus builds?
If you use or are considering Shopify Plus, ask this.
Checkout.liquid got deprecated in March 2024 for 99% of merchants. The replacement, Checkout Extensibility, is locked behind a Shopify Functions and UI extension-based app system. This doesn’t allow direct checkout UI changes the way checkout.liquid did.
Shopify Functions are JavaScript snippets that run at checkout, pre-purchase and post-purchase. They’re also completely isolated from the rest of your theme. A checkout UI extension is what allows an app to inject elements or logic directly into the checkout flow.
An agency that’s not well-versed in this newer, app-intermediated version of checkout.liquid is not a contender for a serious Plus build. Ask specifically straight up for examples of how they’ve used Shopify Functions to customize checkout flow and if they’ve created any checkout UI extensions and why.
The work required to migrate your current checkout over from checkout.liquid is not insignificant, so you don’t want a rookie discovery phasing the deprecation process on your time.
6. How do you approach API integrations and middleware strategy?
Most growing merchants need their Shopify store connected to something else – an ERP, a CRM, a custom inventory management system, a third-party logistics provider. These integrations are where projects get complicated and expensive fast if an agency doesn’t know what they’re doing.
The key technical issue to probe here is how they handle Shopify’s API rate limits. Shopify restricts how many API calls a store can make within a given time window. If an agency is building an integration that hammers the API without accounting for those limits, you end up with sync failures, data inconsistencies, and a support headache.
Ask whether the integration requires a custom middleware layer – a separate service that sits between Shopify and the third-party system and manages the data flow. This is often the right answer for complex integrations, and an agency that recommends it unprompted is demonstrating technical maturity. An agency that promises to “connect everything directly” without discussing rate limits or error handling is probably going to create problems.
7. Who owns the code and design assets when the project ends?
This is a key component that needs to be explicitly clear in the contract, yet many merchants overlook it.
The outcomes of any custom Shopify project – the custom code, the custom apps, the design files, the Liquid templates – need to be entirely owned by you when the project becomes final. A few agencies will draft a contract that allows them to keep IP rights to the code, which puts you at a disadvantage if you ever decide to switch agencies or take development internally.
Make sure you get a look at the IP ownership clause before you put pen to paper. If they resist transferring full ownership to you, find another partner.
8. What does your post-launch support and SLA look like?
Once your custom build is live, the real work begins. Bugs come to the surface after launch, and small updates can cause major issues. Part of the Shopify ecosystem is an ever-burgeoning release of updated themes and features, all requiring regular security maintenance for optimum performance.
To be sure your site is running as smoothly as possible post-launch, you need a maintenance plan in place. Most agencies offer a 30- or 60-day warranty period after the site goes live to address any bugs in the original development. After that, it becomes either an hourly rate or a monthly subscription-based rate to retain their services.
9. How do you handle scope creep and change requests mid-project?
Scope creep can cause a fixed-price project to become a situation where the bills keep coming. Suddenly, requirements multiply, features grow based on the client’s needs, and the project is 40% more expensive without any clear solutions in sight.
Inquire how the agency manages changes. How does the process work when you want to add a feature that wasn’t part of the original agreement? How do they determine the new scope, cost, and ratification of such requests? How are the necessary modifications to the scope documented?
A professional agency will have a change order system in place. They will carefully outline the original plan and generate change orders for any new work that is needed, including an estimated cost and deadline, and receive written approval before proceeding. An agency responding with “We will just see how things go” doesn’t really have a project management system but rather plans to charge you for the process in the future.
10. What does the handover and training process look like?
This is a question most merchants forget to ask, and it might be the most expensive oversight.
When the project wraps, you need to be able to manage the store internally without resorting to calling the agency for every minor update. This means requesting the agency to provide documented walk-throughs of how to update copy, swap images, order content, and configure new product templates using the theme editor for all custom sections they built in your store. Video walk-throughs are far more useful than written docs if your staff is non-technical.
Ask to see an example of hand-over documentation from a previous project. If they don’t have a standardized hand-over process, you’re going to end up unwittingly entering a content-management dependency with the agency for simple tasks. That’s not a partnership. That’s a subscription you didn’t know you signed up for.
Choosing an agency worth your trust
Not every agency will meet all these criteria, but that’s fine as long as you feel comfortable with their explanations of how they operate instead. A good relationship between a company and a development provider is about openness, honesty, and trust, and the only way to establish those things is through frank dialogue.
