3 Critical Mistakes to Avoid When Migrating to Shopify

Replatforming to Shopify or Shopify Plus is a turning point for many e-commerce businesses.

Brands migrating from Magento, WooCommerce, or custom-built solutions choose Shopify for its modern architecture, strong performance, streamlined backend, and robust app ecosystem.

But the migration process is more than just moving your store to Shopify.

It’s a strategic opportunity to rethink performance, and a potential risk if done without proper planning.

At craftberry, we’ve led over 100 complex Migrations to Shopify.

And across industries, the same 3 mistakes when migrating to Shopify keep showing up.

In this article, we dive into the Shopify migration process - unpacking the common challenges, hidden risks, and how to avoid costly issues before they happen.

The Shopify migration process is more than moving data from one e-commerce platform to another.

It includes rethinking how your store data, design, and integrations work together on the Shopify platform.

A successful Shopify migration requires a detailed approach that covers everything from store data and design to redirects, integrations, and backend performance.

The migration process typically includes:

• Preparing and transferring your customer data, product listings, orders, and collections
  
  

• Setting up 301 URL redirects to prevent SEO issues and avoid traffic loss from broken links
  
  

• Rebuilding key store functionality using Shopify-native logic or Shopify apps
  
  

• Testing every customer-facing flow (from product search to checkout) for accuracy and performance
  
  

• Verifying that your theme files, settings, and third-party tools are optimized for the new platform

Every e-commerce platform structures data differently.

So migrating from Magento, WooCommerce, or a custom-built site often requires more than just uploading CSV files.

You’ll need to identify gaps, clean legacy data, and adapt logic to fit Shopify’s structure.

The more complex your existing store, the more planning and validation the process will require.

Working with experienced migration experts helps minimize risk and ensures no critical steps are overlooked during the transition.

When done right, the migration creates a more scalable, stable, and user-friendly Shopify store that supports better customer experience, faster performance, and smarter growth.

Below, we cover the 3 most common mistakes that store owners make during this transition - and how to avoid them.

A platform migration is often seen as the ideal time to refresh the storefront.

While redesigning can improve performance, doing it without a clear understanding of what’s already working introduces unnecessary risk.

Many brands make major visual and structural changes, such as removing search functionality, altering navigation hierarchies, or replacing high-performing PDP elements, without consulting actual user behavior data.

This often leads to a drop in conversion rate, reduced usability, and a disconnect between the new store and established customer expectations.

• Analyze the existing store using tools like GA4, heatmaps, and session recordings to understand what drives engagement
  
  

• Preserve proven UX flows and patterns identified through customer data
  
  

• Redesign only where needed, focusing on underperforming elements
  
  

• Gather qualitative insights through on-site surveys or post-purchase feedback

Any visual changes should also align with your existing brand identity, maintaining consistency across touchpoints to retain customer recognition.

A smooth migration protects both brand consistency and conversion performance.

Every ecommerce platform handles URLs differently.

When moving to the Shopify platform, old URL paths may no longer exist, making proper redirection essential.

If 301 redirects aren’t set up correctly, the result is a cascade of broken links, 404 errors, and lost organic traffic.

Search engines interpret this as a drop in site reliability, which directly impacts SEO ranking and visibility.

In the first few weeks after launch, traffic declines are often tied to missing or misconfigured redirects.

• Use GA4 or previous analytics tools to identify top-performing URLs from the existing site
  
  

• Plan 301 redirects to point each old URL to its new equivalent in the Shopify store
  
  

• Implement redirect automation using a reliable Shopify app like Easy Redirects
  
  

• Monitor post-launch activity and configure fallback redirects to capture any unmapped traffic

It is not just a technical step; it’s a critical part of preserving long-term SEO value and maintaining customer trust.

A successful data migration goes beyond simply exporting and uploading CSV files.

Every ecommerce platform structures and stores information differently, and migrating to Shopify requires aligning that data with Shopify’s native logic.

Incomplete or improperly mapped data can result in missing customer records, broken order histories, invalid discount codes, and lost store assets like product tags or metafields.

For any online business, these issues can lead to customer service friction, inaccurate reporting, and unnecessary operational overhead.

Mismatched or missing data can also impact inventory management, leading to fulfillment delays and customer dissatisfaction post-launch.

• Validate customer data, ensuring order history, purchase tags, and address details are transferred correctly
  
  

• Rebuild discount rules natively in the new Shopify store and test them across use cases
  
  

• Identify and reconfigure custom metafields and data logic from the previous platform
  
  

• Use migration tools like Matrixify to manage high-volume data migration accurately

Thorough planning and testing help avoid the hidden pitfalls of poor data handling and create a stable foundation for growth on the Shopify Plus platform.

For brands migrating from platforms like Magento or WordPress, Shopify offers the flexibility and performance needed to support a high-performing store.

But the migration journey is more than just switching tools, it’s about building a new site that’s easier to manage, maintain, and optimize.

With the right approach, your store doesn’t just move, it evolves.

At craftberry, we bring over 9 years of technical expertise in Shopify Plus and high-performance ecommerce platform builds.

Our team handles everything in-house - from UX and theme development to data migration, SEO, and post-launch monitoring.

If you're switching to a new ecommerce platform, craftberry helps you protect your SEO, avoid data loss, and launch with confidence.

Book a free appointment to discuss how a well-planned Shopify migration can set your store up for long-term performance and growth.

Read more: Shopify vs WooCommerce