10 technical challenges nobody tells you about building your first Shopify app

So you’re ready to build your first Shopify app. You’ve got a unique angle, you’ve planned all your fanciest features, and you want to start solving real merchant problems.
When you're planning your first Shopify app, it's easy to get distracted by all of the fun, interesting features you want to build and forget about the more mundane technical implementation details.
But before you get to the good stuff, you’ll need to make sure you have the basics covered. We’re here to walk you through the essential components that will set your app up for success in the Shopify ecosystem.
1. Rock-solid authentication
This isn’t a nice-to-have— it’s a requirement. Your Shopify app needs bulletproof authentication from day one. This means proper OAuth implementation, secure session management, and careful API token handling. Don't cut corners here – authentication issues can compromise merchant data and trust, and your app should handle authentication edge cases gracefully.
Beyond basic OAuth, you need proper session token handling for embedded apps and secure API authentication for backend requests. You can use modern development platforms (like Gadget) to handle most of this complexity for you, but it’s always helpful to understand how it works.
2. Reliable webhook processing
Webhooks are how Shopify tells your app about changes in a merchant's store. You need reliable webhook processing that can handle out-of-order delivery, duplicate webhooks, and Shopify's rate limits. Build in proper retry logic and keep track of webhook processing status to maintain data consistency.
Remember that webhook processing needs to scale independently of your admin interface — and Shopify stores can have massive traffic spikes during sales and events. Build your webhook handlers to work asynchronously and implement proper queuing to handle high-volume periods like BFCM.
3. Embedded admin interface
Although some developers have had success with standalone apps, most merchants expect your app to integrate seamlessly with Shopify's admin. This means building an embedded interface that follows Shopify's design patterns and performance requirements — and that can be challenging.
Your admin interface needs to achieve an LCP score under 2.5 seconds and follow Shopify's security requirements for embedded apps. Use Shopify's Polaris components to maintain consistency with the platform's design patterns.
4. Reliable support system
Merchants expect prompt, helpful support when issues arise, so make it easy for them to contact you when things go wrong. Build support tools into your app from the start, adding features like error reporting, diagnostic information, and self-help resources. These help you see where and when users are having trouble, which can allow you to prioritize features as you grow.
If you’re short on staff but still want to offer personal support, look into using an AI agent. With the advancements in AI over the past few months, you can train your own GPT to understand your app’s core functionality. Let a bot handle the low-level problems, while you step in to take over more complex complaints.
5. Good documentation — for you and users
Give your merchants the tools to help themselves. Good documentation saves both you and your merchants time, so it’s worth documenting your app's features, configuration options, and common troubleshooting steps to avoid getting bogged down with support tickets. If you’re using AI for support, you can use the documentation to help train it to fully understand your app!
Make sure to keep your documentation up to date as your app evolves — you may even want to add video tutorials or interactive guides for complex features where you know users are likely to get stuck.
Proper documentation isn’t just for your end users. As your app grows, you may want to bring on other developers, or revisit old code you wrote months or years ago. By keeping your code well documented, you’ll avoid unnecessary rabbit holes and save on the cost of development hours down the road.
6. Clear merchant onboarding
First impressions matter. Create a clear onboarding flow that helps merchants understand your app's value and get started quickly.
Consider building an onboarding checklist or wizard that guides merchants through initial setup. Make it easy for them to verify that your app is working correctly. And don’t underestimate the power of a welcome email — you can set the tone for future customer interactions by sending a simple automated message when you get a new install.
7. Proper error handling
Things will go wrong – APIs will time out, requests will fail, and data will be invalid. Your app needs to handle these scenarios without disrupting a merchant's business.
Common areas where you'll need robust error handling include webhook processing, API calls to Shopify, and user interactions in your admin interface. Build retry logic with exponential backoff for API failures, implement proper queue handling for failed webhook processing, and make sure your frontend gracefully handles backend errors.
Remember that error messages need to be helpful for both merchants and your support team. A generic "Something went wrong" message isn’t helpful for anyone — users feel abandoned, and it makes troubleshooting nearly impossible. Log detailed error information for your team while showing merchants clear, actionable messages about what went wrong and what they can do about it.
8. Efficient data synchronization
Most apps need to maintain some local data from Shopify. Build efficient sync processes that handle Shopify's rate limits and eventual consistency model.
The challenge isn't just getting the data – it's keeping it accurate over time. Shopify's webhooks don't always arrive in order, and sometimes they don't arrive at all. Your sync process needs to handle these edge cases without corrupting your local data.
Initial data sync during app installation is particularly tricky. You're limited to 2 requests per second, so syncing a large store's historical data can take hours. Build your sync process to be resilient to interruptions and make sure merchants understand what's happening during long sync operations.
9. Comprehensive monitoring
You need visibility into how your app is performing. This means more than just watching for server errors – you need to track key metrics that indicate your app's health and performance.
Set up monitoring for critical paths like webhook processing, API response times, and database performance. Watch for trends that might indicate emerging problems, like gradually increasing response times or subtle increases in error rates.
Make sure you can correlate issues across different parts of your system. When a merchant reports a problem, you should be able to trace their actions through your logs and quickly identify what went wrong.
10. Scalable infrastructure
Build your app to handle growth from the beginning. This means thinking carefully about database design, implementing proper indexes, and setting up efficient caching strategies. Shopify will occasionally feature new apps in the spotlight on the app store to help with discovery, so you’ll want to be ready from day one.
Many apps hit their first scaling challenges during high-traffic periods like Black Friday/Cyber Monday. Suddenly your webhook processors are backed up, your database is struggling, and merchants are experiencing delays. Plan for these scenarios from the start by implementing proper queuing, using background jobs effectively, and ensuring your database can handle spikes in load.
Remember that scaling isn't just about handling more traffic – it's about maintaining performance as your data grows. Queries that work fine with 100 records might grind to a halt with 100,000. Design your database schema and queries with this in mind, and regularly test with realistic data volumes.
Building Shopify apps can be overwhelming, but you can rest assured knowing that you’re joining an amazing community of builders. Don’t be afraid to ask questions and reach out for help when you get stuck. You’ll need to pay close attention to both technical details and merchant needs, so focus on building reliable core functionality before adding complex features.
If you want to skip all of the tedious setup, you can build your first Shopify app with Gadget to get these essential features built in — the platform comes with auto-scaled infrastructure, automatic documentation, and will even handle detailed work like Shopify OAuth, webhook management, and background jobs.
We’re always available to answer any questions over in our Discord community, where you can learn from other developers building Shopify apps.