7 Costly Mistakes to Avoid When Migrating to Shopify Plus

7 Costly Mistakes to Avoid When Migrating to Shopify Plus

A business starts with a small website… fewer products and less investment. But as soon as traffic spikes, the website stops supporting, and revenue takes a hit.

This is exactly what happened with Kylie Cosmetics before they decided to migrate to Shopify Plus.

When they launched their first limited-edition product, the website crashed. Read more here.

If you’re considering migrating to Shopify Plus, you're choosing a platform built for scalability, to take your growth as far as it can go.

But here’s the thing: Even the right decision won’t deliver the right results if it’s done wrong.

And after migrating over 6,000 stores to Shopify and Shopify Plus, we’ve seen a pattern of costly mistakes that many brands make, and that you should absolutely avoid.

So, let’s get started with the heaviest question of all - 

Should I migrate my store to Shopify Plus?

Because the biggest mistake you’d make is making a decision without carefully considering. So let’s find the answer.

Should You Migrate Your E-commerce Store to Shopify Plus?

Shopify Plus is built for brands that are scaling fast, handling high volumes, or need more customization, automation, and control. But that doesn’t mean it’s for everyone.

But if you’re hitting tech limitations, dealing with checkout restrictions, managing multiple stores or international markets, or simply growing faster than your current setup can handle, then yes, it might be time.

The mistake is not in making the decision.

The mistake is in thinking the decision alone is enough.

Because even the right move can fall apart if the migration itself isn’t done right.

So, ask yourself if I am ready. And if yes, let’s look at the classy mistakes you must avoid - we have helped several businesses when they hit these bumps in the road while migrating to Shopify Plus.

Common Shopify Migration Mistakes

Over the years, we’ve had brands come to us years after their migration, asking why their store isn’t performing the way it should.

Sometimes, the migration was done in-house. Sometimes, it was handled by an agency. But the issues are usually the same, avoidable mistakes made during the move that no one caught in time.

Let’s look at these mistakes - avoidable but costly when made.

Mistake 1: Not Planning a Complete Data Migration Strategy

Data is one of the most valuable assets in E-commerce, but it’s also one of the easiest to mishandle during migration. The assumption that it’s just a matter of exporting and importing spreadsheets is where most mistakes begin.

A complete migration isn’t just about products and customers. It includes order history, customer tags, discount setups, gift card balances, subscriptions, custom fields, media, and not all of it fits neatly into a CSV.

Some brands end up migrating everything, even the clutter they don’t need. Others skip over critical fields that quietly break the store later. We’ve seen both cases, and the issues usually show up weeks or months after launch.

The right approach is simple: audit everything before you move anything. Use Shopify’s native tools where you can. For the rest, especially subscriptions or custom data, test in a staging environment. And if your team isn’t familiar with Shopify’s data structure, get help from a trusted Shopify Plus Agency early. A wrong decision at this stage can quietly affect how your store runs every single day.

Mistake 2: Not Handling Redirects and SEO Properly

SEO rankings are hard earned and losing them can cause a long-term dent in your search visibility, traffic, and revenue.

While migrating to Shopify, SEO deserves special attention. It’s not just one step in the process, it’s a process on its own.

Many brands assume SEO will “just come along for the ride,” but that’s not how it works. Every URL that changes, product pages, collections, blog posts, needs a proper 301 redirect pointing to its new location. Without these redirects, search engines see your new pages as brand new, and your old SEO value disappears overnight.

It’s not just about redirects, though. Meta titles, descriptions, and structured data need to be carefully moved or rebuilt to keep rankings intact. Even minor changes in URL structure or page load speed can impact SEO performance.

The best way to avoid surprises is to start with a full SEO audit before migration.
Map every old URL to the new one. Use tools like Google Search Console and Screaming Frog to monitor broken links and crawl errors. And after launch, keep an eye on your traffic, dips might mean something slipped through the cracks.

SEO migration isn’t glamorous, but it’s the foundation of keeping your store visible and profitable.

Pro Tip: When choosing a Shopify Plus agency for your store migration, go for a partner with in-house digital marketing expertise.

Because SEO during migration isn’t just a checklist item, it’s a high-stakes process. Agencies with dedicated SEO teams understand how to handle redirects with precision, preserve crawl equity, and account for Google’s ever-changing algorithm updates, all while being deeply familiar with how Shopify Plus structures URLs, handles meta fields, and supports custom Shopify SEO setups.

They won’t just move your store, they’ll make sure your visibility doesn’t take a hit along the way.

Mistake 3: Overengineering with Too Many Apps & Scripts

One of the easiest ways to slow down a freshly migrated store is by installing every app “just in case.” We see this all the time, brands stacking multiple apps for bundling, upselling, reviews, loyalty, analytics, and custom functionality. The logic is simple: install now, optimize later. 

But the results aren’t always what they want - and usually is the opposite - a bloated backend, slower load times, overlapping features, and conflicts that are harder to trace.

The truth is, not everything needs an app, especially on Shopify Plus. With Shopify Functions, Flow, and native extensibility features, much of the functionality you’re paying for through apps can be built more efficiently and securely.

This mistake isn’t always on the merchant either, sometimes it’s the agency or developer trying to shortcut timelines. But adding complexity early always costs more later, whether in performance, maintenance, or rebuilds.

Before you migrate, define exactly what the store needs to do, and explore what can be handled natively or with lean custom code and discuss it in detail with your Shopify Plus Agency or the development partner. Apps should solve problems, not create new ones.

Mistake 4: Not Rebuilding Custom Functionalities the Right Way

One of the most common pain points we see post-migration? Custom features that worked fine on the old platform… and now either don’t exist or don’t work as expected.

Shopify Plus isn’t a copy-paste solution, it’s a different architecture entirely. If your previous store ran on custom logic for pricing rules, subscriptions, bundles, or multi-step checkout flows, that logic has to be rethought, not just replicated.

Many brands try to “bring over” functionality as-is, without considering how Shopify handles things differently. What worked through plugins or code hacks on Magento or WooCommerce might need to be rebuilt using Shopify Functions, Flow, or Checkout Extensibility.
If you skip that step, things start breaking quietly: discount rules don’t apply, carts behave oddly, or the checkout experience feels off.

Rebuilding the right way isn’t just about keeping things functional, it’s about adapting to Shopify’s way of doing things. It’s cleaner, more stable, and gives you better performance in the long run. But only if it’s done deliberately.

Mistake 5: Ignoring Theme Architecture and Shopify 2.0 Structure

Some themes look good but can still be slow as a slug. 

With the release of Online Store 2.0, Shopify completely changed how themes are structured, but not every store upgrade catches up to it.

Often while migrating to Shopify Plus, brands carry over their old theme setups without revisiting how content, layouts, or customizations should now be managed. A 2.0 theme isn’t just a visual refresh, it's an entirely different foundation. And if you’re not using it right, you’re adding unnecessary limitations.

What does that look like in practice?

Static templates with hardcoded sections. Content that needs developer support to update. Apps were forced into the layout because app blocks weren’t utilized. No use of JSON templates or dynamic sections.

This defeats the purpose of 2.0 entirely.

The better approach?

Use the 2.0 architecture as intended. Set up reusable sections. Make your theme scalable. Align layout logic with your team’s content workflow. Give marketers control where they should have it, and developers space to focus where they’re needed most.

Migration isn’t about copying over your site, it’s a chance to rebuild it with better bones.

Mistake 6: Neglecting Performance Optimization Post-Migration

A migration might get your store up and running on Shopify Plus, but that doesn’t mean it’s running well.

One of the most overlooked steps after a successful migration to Shopify Plus is performance optimization. Teams are often so focused on getting every feature and page live that they miss what actually matters to the end user: speed, responsiveness, and stability.

Even a well-built Shopify Plus store can suffer if assets aren’t compressed, third-party apps slow down load times, or scripts conflict with one another.

Many stores migrate to Shopify Plus for better performance, but if optimization is skipped, they barely see the difference.

What needs attention?

• Image sizes and lazy loading

• Unused app scripts or leftover code from the old platform

• Code minification and critical CSS

• Liquid logic and theme bloat

• Mobile responsiveness

If the site loads slowly or feels clunky, users bounce, no matter how great the backend setup is.

The takeaway:

Migration isn’t the finish line. It's the starting point. Optimize your storefront like you would tune a high-performance engine, only then will you get what you came for.

Mistake 7: Skipping QA for Checkout, Mobile, and Custom Logic

For most brands migrating to Shopify Plus, launch feels like a checklist, good design, integrated features, done. But the moment the site goes live, reality hits.

An email lands in customer support: “My payment got deducted, but I didn’t get an order confirmation.”
Then another: “The subscription option isn’t working.”
Then: “Why isn’t the discount code applying?”

Soon, the inbox is overflowing.

Can you guess what went wrong?

They skipped proper QA.
A classic oversight, and one that can quietly cost brands a fortune.

When you’re rebuilding or migrating to Shopify Plus, there’s more to test than just how things look.
You need to simulate real user flows: checkout logic, subscriptions, third-party apps, custom code, mobile responsiveness, and even discount rules. One broken link in the chain, and your revenue takes the hit.

The right approach? Treat QA like launch insurance.
Test every flow, logged-in vs guest checkouts, mobile vs desktop, edge cases with discounts and gift cards. Don’t rely on assumptions. Rely on staging, sandbox testing, and checklists designed for eCommerce logic.

It’s not overcautious. It’s smart. Because the one thing worse than a delayed launch… is a broken one.

Bonus Section: Business Mistakes That Still Break Stores

These aren’t always on the developer’s plate, but they hit just as hard if missed.

• Migrating during peak sales season
  Launching during your busiest time of year, like Black Friday, a new collection drop, or the holiday season, is a high-risk move. Even small bugs can lead to big revenue losses when traffic is at its peak. Always plan your store migration during a quieter period, so you have breathing room to test and fix things.

  
  

• Launching without team training
  A new platform means new processes. If your internal teams, like customer support, fulfillment, or marketing, haven’t been trained on how the new backend works, they’ll struggle to keep up. That can slow down order processing, lead to mistakes, or frustrate customers who need help.

  
  

• Breaking the customer loyalty experience
  Many brands forget to migrate loyalty data properly, reward points, gift cards, saved accounts, subscription preferences. If customers log in and find their information missing, their trust in your brand takes a hit. It’s not just a technical loss, it’s a customer relationship one.

  
  

• Copy-pasting old UX
  Rebuilding your store on Shopify Plus isn’t just a technical move, it’s a chance to rethink how your site works. Simply copying the old layout and flow often means carrying over outdated design patterns, poor mobile experience, or clunky checkout logic. It’s a missed opportunity for improvement.

  
  

• No strategy around expansion (multi-store, multi-language, multi-currency)
  If you’re planning to go global, your migration should reflect that. Setting up multiple stores, offering localized languages or currencies, or managing tax differences across regions, these things need a clear plan. Trying to add them later makes the setup more complicated and expensive.

  
  

• Treating Shopify Plus like “just another version” of Shopify
  Shopify Plus is built for scale, with tools like automation (Shopify Flow), advanced APIs, and exclusive access to features like Launchpad, checkout customizations, and dedicated support. Using it the same way you used a Basic plan means you’re not getting the value you’re paying for, and likely missing efficiencies that could streamline your business.

Our Two Cents 

Now that you know the common mistakes brands often make while migrating to Shopify Plus, you're already equipped with the knowledge to avoid them. That’s a powerful place to be.

We suggest treating migration not as a technical upgrade, but as a strategic transformation. One where timing, SEO, data structure, app dependencies, and customer experience all play a role. It’s not just about moving, it’s about moving with precision. A rushed migration can quietly undo years of digital growth. A well-planned one, however, can set the stage for scale, speed, and smarter selling. So before you dive in, take a moment. Reassess. Plan it like your next big campaign, because, in many ways, it is.

Planning to Migrate Your Store to Shopify Plus? IT Geeks Can Help!

At IT Geeks, as Shopify Premier Partner we don’t believe in pushing businesses into migrations. Instead, we help them step back and evaluate if Shopify Plus is the right move, right now. If it is, we build a migration plan around their store’s specific needs: the structure, the scale, the tech stack, the team. And if it isn’t, we tell them that too.

Because we know a migration only works when it aligns with your goals, not just your growth charts. So let’s talk. No pressure, no selling. Just an honest conversation with people who know what’s at stake.