How to Migrate Integrations Between Shopify and Magento

Migrating from one e-commerce platform to another is never as simple as “export and import.” If you're trying to migrate integrations from Shopify to Magento, you're dealing with synced apps, automation rules, APIs, customer data, tags, product metadata, and workflows that power your sales engine. One wrong move and your entire store can face downtime, broken customer journeys or data inconsistencies.

The good news? A structured approach can make this migration smooth, predictable, and low-risk.

In this guide, you’ll learn exactly how to migrate integrations (Shopify to Magento) step-by-step, with actionable takeaways, examples, and key pitfalls to avoid.

Why Migration Is More Complex Than Moving Storefront Data

A case study on J.Lindeberg, a high-end fashion and sportswear brand, illustrates how it replatformed its e-commerce store to Shopify Plus in just 16 weeks, transforming the site into a visually rich, brand-driven experience and boosting revenue by 70%, with a 7% rise in both conversion rate and average order value. 

This means that e-commerce platform migration isn’t just about products and orders. Your Shopify integration stack (from email platforms, CRM, analytics tools, inventory systems, loyalty apps to support tools) must be mapped and rebuilt on Magento without disrupting customer experience.

A structured system ensures:

• No duplicate customer profiles

• No missing product links

• No broken API calls

• No loss of automation flows

Here’s a step-by-step guide to e-commerce platform migration. 

Step 1: Audit Your Existing Shopify Integrations

Before you migrate integrations Shopify to Magento, conduct a full audit of what you currently have in Shopify. List:

• Marketing automation tools (Klaviyo, Mailchimp, Meta ads, Google Ads)

• Analytics + tracking (GA4, server-side tracking, pixel apps)

• ERP / Inventory systems

• CRM integrations

• Shipping + fulfillment apps

• Customer communication tools (support desk, chatbots)

Pro Tip: Use Shopify’s built-in “App Usage Reports” to see which integrations actively process data.

This prevents over-migration and helps identify tools you no longer need.

Step 2: Map the Data for Shopify–Magento Migration

A common mistake during e-commerce platform migration is assuming Shopify data fields match Magento fields 1:1, because they rarely do.

For example:

• Shopify “Tags” → Magento “Attributes”

• Shopify “Collections” → Magento “Categories”

• Shopify product variants → Magento configurable products

When planning Shopify Magento data migration, map the following:
✔ Customers
✔ Orders
✔ Product metadata
✔ Discounts & rules
✔ Automation triggers
✔ App-specific custom fields

A structured data map ensures that integrations relying on these fields continue functioning after migration.

Step 3: Ensure API Compatibility Before Rebuilding Integrations

Each platform’s API behaves differently:

• Shopify: REST + GraphQL with strict throttling

• Magento: REST + SOAP APIs with customizable endpoints

Before you migrate integrations Shopify to Magento:

1. Check whether your current apps offer Magento-compatible versions.

2. For custom integrations, verify Magento’s API endpoints.

3. Test authentication methods (OAuth, token-based access).

Step 4: Recreate Automation Workflows in Magento

Automation is the lifeblood of modern e-commerce. During Shopify integration migration, merchants often forget workflow recreation until late, which leads to gaps like:

• Abandoned cart emails not firing

• Loyalty points not syncing

• Retargeting audiences breaking
  
  
  

Here is a checklist for workflow migration:

• Customer segmentation rules

• Event-based triggers

• Email/SMS automation

• Audience syncing with Meta + Google

• Inventory + order sync cycles

Step 5: Test All Integrations in a Staging Environment First

Never connect integrations directly to the live Magento store. Magento's architecture is more configurable, but that also means things break more easily if untested.

Test the following in staging:

• Inventory sync

• Customer creation

• Order creation + payment confirmation

• Marketing events (viewed product, added to cart, purchase)

• Third-party API event passing

Research by the Baymard Institute shows that 20% of users abandon carts due to errors or friction during purchase. Testing integrations prevents these errors from appearing in production.

Step 6: Switch Integrations to Magento With Zero Downtime

Once staging is stable:

1. Freeze data changes for high-volume datasets (orders, products).

2. Run a final sync.

3. Switch API endpoints from Shopify to Magento.

4. Monitor logs for 24-48 hours post-migration.
   
   
   

This ensures clean and continuous data flow across all tools. 

Pro tip: You may want to integrate social commerce into  your Shopify and Magento stores to boost conversion. 

FAQ: Migrate Integrations Shopify to Magento 

1. How long does it take to migrate integrations Shopify to Magento?
Most mid-size stores take 2–6 weeks depending on integration complexity.

2. Will my automation workflows break after migration?
If not rebuilt correctly, yes. Always recreate workflows tailored to Magento events.

3. Can all Shopify integrations be replicated in Magento?
Most can. For unsupported tools, middleware connectors or custom API integrations can fill the gap.

4. Is it possible to migrate customer tags from Shopify to Magento?
Yes, but they usually map to Magento attributes or customer groups.

Final Thoughts

Migrating integrations Shopify to Magento doesn’t have to be chaotic. 

With the right planning, data mapping, API validation, and testing workflow, your migration can be seamless and even improve performance. Treat this migration as an opportunity; not just to rebuild your stack, but to optimize it.

If you're moving from Shopify to Magento, Markopolo can act as a unified intelligence layer that keeps your customer data consistent, clean, and trackable across both platforms before, during, and after migration. Book a call to find out how.