Merchants leave Magento for good reasons: the cost of hosting and maintaining it, the specialist developers required for routine changes, the security patching burden, and the infrastructure overhead. Shopify removes all of that. But Magento stores are also typically the most heavily customised in e-commerce, and that customisation is exactly what makes the migration complex.
This article covers the specific things that break or require careful handling when moving from Magento to Shopify, so you can plan for them rather than discover them.
1. Complex catalogue structures do not map cleanly
Magento's catalogue model is more complex than Shopify's. Magento supports configurable products, bundled products, grouped products, and custom attribute sets that can create product structures with no direct Shopify equivalent.
What this means in practice: a Magento configurable product with many custom attributes may need to be restructured to fit Shopify's product and variant model. Shopify has a limit on variants per product and a different approach to product options. Products that exceed these constraints or rely on Magento-specific structures need a deliberate remapping strategy.
The fix: map your Magento catalogue structure to Shopify's model during planning. Identify products that will not translate directly and decide how to restructure them before the migration, not during it.
2. Custom attributes and EAV data
Magento stores product data in an EAV (Entity-Attribute-Value) model, which allows extensive custom attributes. Stores often accumulate dozens of custom attributes over years of use. Shopify handles this differently, using metafields.
Every custom Magento attribute needs a decision: does it map to a native Shopify field, a metafield, or is it no longer needed? A store with 40 custom attributes cannot simply export and import - each attribute needs mapping to Shopify's structure, and the ones that carry SEO or operational value need particular care.
The fix: audit every custom attribute during discovery, map each to its Shopify destination, and validate that the data transfers correctly with meaning intact.
3. URL structure differs completely
Magento's URL structure - including its category-path URLs and URL suffixes like .html - differs fundamentally from Shopify's. Every Magento URL will change, which makes the redirect map both essential and substantial.
Magento stores often have deep category hierarchies reflected in their URLs, and product URLs that include category paths. Shopify uses a flatter, different structure. Mapping these requires care, especially where a single Magento product was accessible via multiple category-path URLs.
The fix: build a comprehensive 301 redirect map that accounts for Magento's URL patterns, including the .html suffix and category-path structures. This is the highest-priority SEO task in a Magento migration.
4. Custom functionality needs re-implementation
Magento's flexibility means merchants often build custom functionality directly into the platform - custom checkout logic, custom pricing rules, custom catalogue features. None of this transfers. Each piece of custom Magento functionality needs a Shopify equivalent: an app, a native feature, Shopify Functions, or custom development.
| Functionality | On Magento | On Shopify |
|---|---|---|
| Custom pricing rules | Built-in module | Functions or custom app |
| Complex catalogue logic | Custom code | Apps or custom development |
| Custom checkout steps | Fully customisable | Plus checkout extensibility |
| B2B account features | Native B2B | Plus B2B or custom |
| Custom integrations | Direct code | Apps or custom API integration |
The fix: inventory every piece of custom functionality during discovery and identify its Shopify path before committing to a timeline. Custom functionality discovered mid-migration is the most common cause of Magento migration overruns.
5. Extensions do not transfer
Magento extensions and Shopify apps are completely different systems. A Magento store running 15 extensions cannot carry any of them across. Each extension's function needs a Shopify equivalent identified and configured.
This is often a hidden benefit rather than only a cost - many Magento extensions exist to add functionality that Shopify provides natively or through better-maintained apps. But every one needs a deliberate replacement plan.
6. Order and customer history at scale
Established Magento stores often have years of order history and large customer databases. Migrating these at scale requires careful handling to preserve data integrity - order statuses, customer tags, historical records, and the relationships between them.
Customer passwords cannot transfer from Magento to Shopify for security reasons. Customers will need to reset passwords on first login - a communication task that needs planning before launch.
The pattern with Magento migrations: the theme build is the easy part. The complexity is in the catalogue mapping, custom attribute handling, functionality re-implementation, and URL redirects. Budget your discovery and planning accordingly - it is where a Magento migration is won or lost.