Migrating Your eCommerce Store: Common pitfalls and how to avoid them

Introduction 

Migrating your eCommerce store from Magento to Shopify can be exciting. It’s a chance to refresh the look and feel, modernise your approach, streamline your processes and position your brand for futrgrowth. 

But, like moving house, it’s also a complex process with many moving parts. 

That means that unfortunately, even with careful planning, scoping, and testing, unexpected challenges can arise; things go missing, get broken and small oversights can become costly mistakes.

And, like moving home within all aspects of the process, there are common pitfalls to avoid.

In this guide, we’ll explore the most common challenges brands face during platform migration and show you how, with the right support you can navigate them successfully.

Our Magento to Shopify migration framework

Before diving into the pitfalls, it’s worth noting that a seamless migration isn’t achieved through luck, rather, it’s the result of a structured, tested process.

At SOZO, we use a proven migration framework, much like relying on a professional removals team who inventories, protects, and transports your belongings safely.

1. Discovery and technical auditing

We examine your entire Magento setup; your catalogue structures, extensions, data quality, integrations and SEO performance, to understand exactly what’s being moved and what condition it’s in.

2. Product catalogue mapping and data cleansing

Just like decluttering before a move, we streamline your catalogue, resolve inconsistencies, map complex attributes, and prepare your data for a clean import into Shopify.

3. SEO and redirect mapping

To protect your search visibility, we map all key URLs, migrate metadata, and plan redirects to ensure your traffic and rankings follow you to your new “address.”

4. Theme and app ecosystem planning

We design your new store environment carefully, selecting the right theme, replacing Magento modules with Shopify-native apps, and identifying any custom features that need rebuilding.

5. Rehearsal migration & testing

Before moving day, we run a full rehearsal migration to verify data, workflows, performance, and integrations.

6. Launch, monitoring and post-migration support

Once you’ve moved in, our team monitors indexing, performance, and user flows, and provides support as your team settles into the new platform.

This approach dramatically reduces risk, ensuring your migration is predictable, stable, and future-ready.

You can read more in our blog: Migrating from Magento to Shopify – A Definitive Guide

Here are some of the common pitfalls of migrating a website:

Data loss or corruption: handling fragile items with care

When you move house, fragile items like fine china or family heirlooms need careful packing. You wouldn’t just throw them into boxes and hope for the best. Your eCommerce store’s data deserves the same level of care.

Product information, customer accounts, attribution and order histories are the backbone of your business. Losing or corrupting these during migration can create chaos: missing product descriptions, incomplete inventory levels, or gaps in customer history can lead to frustrated shoppers and lost revenue.

Even small errors, like mismatched SKUs or missing images, can ripple through your operations and marketing.

The best way to avoid this is through meticulous data management. Clean and audit your data before migration, identify potential problem areas, and use reliable tools or expert partners to manage the transfer. Running sample imports and verifying that everything works correctly before the final move is crucial. 

With careful handling, your data will arrive intact, just like your fragile valuables, and your new Shopify store can start life fully equipped.

SEO and URL issues: ensure your mail is forwarded 

When you move house, you update your address and set up mail forwarding so letters and packages continue to reach you. Skip this step, and important correspondence gets lost.

For your eCommerce store, SEO is your digital address. Every URL, meta title and page description represents a path for customers and search engines to find your business and its products. 

During a migration, failing to manage these redirects properly can have serious consequences. Pages may suddenly disappear from search results, web traffic can drop and even loyal customers may struggle to find your products they once purchased regularly.

To prevent this, create a detailed URL mapping plan before moving. Implement 301 redirects to guide visitors from old URLs to new ones silently in the background, carry over metadata, and ensure structured data is preserved. 

Because some information won’t migrate seamlessly, you may have to also make a plan to migrate blog content, product categories and tags as well. 

This is also an opportunity to improve these elements but that shouldn’t be a blocker to the migration itself.

After launch, you should closely monitor your rankings with tools free like Google Search Console or paid options like SEMRush to catch broken links or indexing errors. You don’t want any forgotten ‘noindex’ commands in place. This way, your Shopify store can hit the ground running, and search engines-like the postman- still know exactly where to deliver to.

Poor site performance: don’t cramp your new space

Imagine moving into a new home and trying to squeeze oversized furniture into awkward corners. Maybe you have lost your flow; daily routines slow down and the space that once worked perfectly now feels inefficient and frustrating.

Your online store behaves similarly. A rushed or poorly managed migration can result in bloat coming over from your old site. You may also find you have poorly optimised images, outdated scripts in Google Tag Manager containers and incompatible embedded widgets and apps in place. 

These elements can slow page load times, frustrate customers, and ultimately reduce conversions on your new site.

It’s always a good idea to test page speed and responsiveness across devices and make adjustments as needed.

A fast, smooth site ensures a better customer experience, higher engagement, and improved sales, just as an organised, uncluttered home makes day-to-day life easier.

Thinking of migrating in the next 6–12 months? Speak with our team to get a plan in place early.

Incomplete feature migration: don’t forget the essentials

It’s always disappointing to unpack your boxes and realise essential items like your fridge, washing machine, or bed didn’t make the move. The same principle applies to migrating from Magento to Shopify.

Not all Magento features migrate directly. Certain custom modules, workflows, or integrations may need to be manually rebuilt or replaced with alternative native solutions. If these are overlooked, your store may launch with missing functionality, frustrating staff and customers alike.

We often have to rebuild custom shipping rules using Shopify’s native functions or apps, replace Magento checkout customisations with Shopify Checkout Blocks and functions and, if necessary, handle customer groups and discount rules separately as part of the migration support.

The solution is a full feature audit before migration. Identify what’s critical for your operations, what can be replaced by a Shopify app, and where custom development may be needed.

Testing workflows before launch ensures nothing essential is left behind, giving your team and customers the same -or even more -reliable experience they had before.

Inadequate Staff training: getting to grips with new technologies

Even the most modern, beautifully designed house can be frustrating if you don’t know how to use its features. Voice-activated lights, smart thermostats, or hidden storage all sound great until you’re unsure how to operate them or the batteries in the controller are flat.

The same goes for your new Shopify store. A powerful platform is only effective if your team knows how to navigate it, manage products, handle orders and leverage the integrated marketing tools. Without proper training, frustration builds, mistakes happen and your store- like your home-doesn’t fulfill its full potential.

To avoid this, invest in structured staff onboarding. Your Shopify partner should provide training sessions, step-by-step guides and ongoing support to ensure your team understands day-to-day processes as well as advanced features. 

A well-trained team allows your new store to run smoothly from day one, just like a household that functions effortlessly in its new home.

Missed optimisation opportunities: renovate while you move

One of the appealing aspects of a Magento to Shopify migration is that theMVP of the replatforming project can be a simple ‘lift and shift’. 

But, one of the joys of moving house is the opportunity to redesign and optimise your new space to suit your needs now and in the future.

Perhaps you buy new furniture for better flow, repaint walls, or install more functional storage. Like buying ‘off plot’, before you move to a new Shopify store you can completely customise your new shop front to reimagine your store’s layout and functionality.

Many businesses make the mistake of replicating what they have using old Magento structures in Shopify without considering the scope for much needed improvement. This is a missed opportunity to streamline navigation, enhance mobile responsiveness, optimise checkout processes and implement new marketing or analytics tools.

By approaching migration strategically, you can renovate while you move, improving both user experience and operational efficiency. The result is a modern, high-performing store that’s easier to maintain and poised for growth-a true upgrade, not just a relocation.

Why Magento 2 Becomes Harder to Maintain Over Time

If this all seems like a lot of effort, it is worth noting that while Magento 2 is an excellent platform, like any beautiful residence, it can become high-maintenance. Over time, many merchants find the upkeep increasingly demanding.

Rising development overheads: Magento requires specialist developers, and their scarcity drives up costs, even for simple changes.

Unexpected bugs after patches: Security patches and version upgrades frequently break custom modules or cause conflicts, making updates stressful and unpredictable.

Slow deployment workflows: Deploying changes requires compilation, cache resets, and extensive testing, slowing your ability to make improvements quickly.

Hosting and server responsibilities: Merchants are responsible for performance, uptime, caching, CDNs, and security, all of which grow in complexity as the store scales.

Custom module upkeep Modules written years ago often need full rewrites to stay compatible, adding ongoing technical debt.

These factors make Magento feel like a property that constantly needs maintenance, draining time, money, and focus. Shopify, by contrast, offers a low-maintenance home that evolves with your business.

What Happens After Launch?

With any migration, there will be anxiety about what happens after the big move day. We know that settling in takes time and that having an expert partner on hand makes a huge difference.

Once your Shopify store is live, SOZO continues to support your growth with proactive, ongoing optimisation.

Our post migration support includes:

Monitoring indexing: We track your SEO health daily, resolving crawl errors, redirect issues, and indexing problems before they impact performance.

Refine site performance: As your store grows, we improve speed, UX, and app efficiency to keep your site running at its best.

Continuously optimise your Shopify ecosystem: Whether you need new automation tools, upgraded search, replacement apps, or custom features, we help you evolve your Shopify setup over time.

Support your team: We provide ongoing training, support, and strategic guidance so your team always feels confident and capable on the platform.

Migration isn’t the end, it’s the beginning of long-term improvement.

Conclusion: move smart, not just fast

Platform migration- like moving house or office location is complex. Even with careful planning, testing, and scoping, challenges can arise. But identifying risks and creating a plan to mitigate them – like handling fragile items, keeping your address updated, ensuring everything fits and works, training the household and taking the chance to optimise the new space can help you navigate the process successfully.

At SOZO, we guide businesses through end -to-end Magento to Shopify migrations. We protect your data, maintain SEO rankings, ensure all critical features are transferred, train your team, and take advantage of optimisation opportunities so your new Shopify store is ready for long-term sustainable success.

Ready to make your move? Book a free consultation with our website migration experts today and start your store’s journey to a faster, more scalable, and smarter home.