Avoid These 7 Common Magento-to-Shopify Migration Mistakes

Thinking of switching your eCommerce store from Magento to Shopify? It’s an exciting move with a lot on the line. On the bright side, re-platforming opens the door to Shopify’s advantages – a more user-friendly, scalable system that frees your team from Magento’s technical headaches and lets you focus on growth.

But beware: a poorly executed migration can cost you dearly, potentially decimating years of hard-earned SEO value and even causing data loss that undercuts your new store’s success.

This isn’t a transition to take lightly. 

The good news is that with careful planning, you can avoid those pitfalls, and this guide will serve as your roadmap to a smooth re-platforming – helping you sidestep the costly errors and land on Shopify with confidence. Your roadmap to a smooth re-platforming—and how to sidestep the costly errors.

Why Migrating From Magento to Shopify Is an Excellent Idea

If you're currently running on Magento, you already know it's powerful—but it comes with trade-offs. Managing infrastructure, relying on developers for updates, and dealing with upgrades can slow down your team and drain resources.

Shopify offers a refreshingly different approach. It’s cloud-based, streamlined, and built for growing eCommerce brands. The benefits aren’t just technical—they show up in performance, agility, and bottom-line impact.

What you gain by migrating:

• Faster time-to-market for campaigns, promotions, and product launches
• Lower total cost of ownership—fewer developer hours, no server fees
• More agility for marketing and merchandising teams to make real-time changes
• Built-in scalability and security, especially with Shopify Plus
• A robust app ecosystem for extending functionality without deep customization
  

In real business terms: 

Brands that switch often see quicker site updates, improved mobile checkout experiences, and reduced dependency on engineering teams—resulting in measurable gains in conversion rates and customer satisfaction.

It’s a smart move. But like any smart move, it requires planning and precision. Migrations can get tricky—especially if you're coming from Magento.

Why Magento-to-Shopify Migrations Are Uniquely Tricky

Not all migrations to Shopify are created equal. Moving from platforms like BigCommerce or WooCommerce can be relatively straightforward. Magento, on the other hand, brings a whole set of complexities that other platforms don’t.

Here’s why Magento-to-Shopify migrations require more care:

• Heavy customization - Magento stores are often deeply tailored, with custom code, modules, and integrations that don’t translate directly into Shopify’s framework.
• Complex data architecture - Magento’s database stores products, orders, and customer info across multiple tables. Migrating cleanly takes extra effort.
• Theme incompatibility - Magento themes aren’t portable. Shopify themes are built with different architecture (Online Store 2.0, section blocks, metafields), so recreating your site’s design takes a fresh build.
• Integration rework - ERPs, CRMs, or payment gateways that connected to Magento may need custom APIs or middleware to work with Shopify.

In short, Magento migrations aren’t “plug-and-play.” They’re rebuilds—and they require strategic execution. If you're unsure, talk to us - we know exactly how to re-platform your site smoothly.

The Most Common Magento-to-Shopify Migration Mistakes (and How to Avoid Them)

1. Skipping or Botching 301 Redirects

The Mistake:

Not properly mapping old URLs to the new Shopify structure.

The Risk:

Loss of organic traffic, broken inbound links, and frustrated returning visitors.

Example: 

If you have many popular blog posts and product pages indexed by Google and shared across social channels, you run the risk of pages returning 404 errors after migration which can severely impact on traffic. Over the next few months, organic traffic could drop significantly, and you may have to begin fielding complaints about “missing” content. Not a good image for your brand!

What to Do: 

Start with a full URL audit. Identify high-traffic pages and inbound links. Use Shopify’s redirect tools or apps to create a comprehensive 301 redirect plan. Test extensively before launch. We can help with that.

2. Overlooking SEO Fundamentals

The Mistake: 

Forgetting to carry over meta titles, descriptions, structured data, and image alt tags.

The Risk: 

Loss of search rankings, reduced discoverability, and long-term traffic decline.

Example: 

If you replatform without correctly preserving SEO metadata, your best-performing product pages could drop out of Google’s top 10, resulting in a significant traffic dip. While paid ad spend could compensate, it’s an unnecessary added expense and your profitability could take a hit regardless.

What to Do: 

Export SEO metadata from Magento and plan how to re-implement it in Shopify—manually or via apps like Matrixify. Keep URL structures consistent wherever possible, and submit updated sitemaps to Google Search Console after launch.

3. Mishandling Product & Customer Data

The Mistake: 

Migrating incomplete or unclean data, leading to broken product listings, missing variants, or lost customer histories.

The Risk: 

Customer frustration, inaccurate inventory, and operational bottlenecks.

Example: 

It’s easy to miss key data when you are importing thousands of products. This could lead to mismatched sizes and stock levels. It could also cause customers to lose access to order histories and saved addresses. The result: a flood of support tickets and a drop in repeat purchases.

What to Do: 

Clean your data before migrating. Run test batches to verify the formatting and accuracy of SKUs, customer profiles, and orders. Use structured import tools and involve customer service and inventory teams in QA.

4. Assuming Themes Transfer Over

The Mistake: 

Trying to replicate your Magento store design pixel-for-pixel in Shopify.

The Risk: 

Delays, budget overruns, and missed opportunities to improve UX with Shopify-native tools.

Example: 

Replicating your Magento design into Shopify using a custom theme rebuild may compromise UX and add weeks to the launch timeline. Not to mention thousands of dollars in development costs. Mostly, companies trying this pivot to a prebuilt Shopify theme and start over.

What to Do: 

Choose a Shopify theme that supports your merchandising goals. Use the migration as a chance to optimize for performance, speed, and mobile experience—not just visual parity.

5. Ignoring Key Integrations Until It’s Too Late

The Mistake: 

Postponing integration planning for core systems like ERPs, CRMs, and payment gateways.

The Risk:

Operational disruption, order fulfillment issues, and fragmented customer data.

Example:

Migrating without confirming your ERP connector’s compatibility with Shopify can result in orders not syncing properly after launch. This can cause inventory mismatches, overselling, and late shipments—hurting both revenue and customer satisfaction.

What to Do:

Audit your current integrations early in the process. Explore Shopify-native solutions, middleware, or custom API work as needed. Build time into the plan for integration testing and stakeholder sign-off.

6. Failing to Test Real Customer Journeys

The Mistake:

Only testing backend workflows without validating what a real customer experiences.

The Risk:

Broken checkout flows, promo code failures, or mobile issues that kill conversions.

Example:

Not checking something like testing discount codes on mobile after migration can result in hundreds of abandoned carts. By the time the issue is discovered, the campaign could be over, with major revenue loss.

What to Do:

Walk through every customer scenario: first-time visitor, returning user, mobile checkout, promo application. Test across devices and browsers. Don’t launch until these flows are clean.

7. Launching Without a Safety Net

The Mistake: 

Going live without a contingency plan or rollback option.

The Risk:

Downtime, revenue loss, and damaged brand reputation if things go wrong.

Example:

If you launch without proper load testing, especially during a major promotional push, the checkout could time out for some users during peak traffic, resulting in thousands in lost sales—and a wave of complaints online.

What to Do:

Build a detailed go-live checklist. Plan your launch during low-traffic hours. Have a rollback strategy and backup plan ready. Monitor analytics and error logs closely in the first 72 hours.

Make the Move to Shopify With Confidence

Moving from Magento to Shopify is one of the smartest steps an ambitious eCommerce brand can take. The gains in performance, agility, and user experience are real and measurable. But success isn’t guaranteed—especially without proper planning.

Avoiding these common mistakes means protecting your SEO, preserving your customer data, and launching a site that works beautifully on day one.

At Total Commerce, we specialize in helping brands execute smooth, efficient Magento-to-Shopify migrations—with the right strategy, structure, and support from day one.

Ready to map out your migration?

Contact us for a free Magento-to-Shopify migration assessment and custom roadmap.