6 January 2026
WooCommerce to Shopify: What Breaks After Migration and How to Fix It
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What Actually Breaks After a WooCommerce → Shopify Migration (And How to Prevent It)
What Actually Breaks After a WooCommerce → Shopify Migration (And How to Prevent It)
The SEO Graveyard: URL Structures and Permalinks
The single biggest asset you risk during a migration is your organic search traffic. If you have spent 5 years blogging and building backlinks to `yourstore.com/blog/category/post-name`, that equity vanishes the moment you switch DNS to Shopify if you are not careful.
Why It Breaks
WooCommerce allows you to define almost any permalink structure you want (`/shop/`, `/store/`, `/product/cat/name/`). Shopify is rigid. It enforces specific prefixes that you cannot change without headless architecture:
- Products live at
/products/ - Collections live at
/collections/ - Pages live at
/pages/ - Blogs live at
/blogs/news/(typically)
The Fallout
If you migrate without a comprehensive redirect 301 map, Google looks for your old high-ranking pages, finds a 404 error, and de-indexes them. You don’t just lose traffic; you lose domain authority.
Prevention Framework: The 301 Map
Do not rely on “wildcard” redirects. You need a 1:1 map.
- Crawl Your Current Site: Use Screaming Frog or Ahrefs to get a full list of every live URL on your WooCommerce site.
- Map to New URLs: Create a CSV. Column A is the Old URL. Column B is the New Shopify URL.
- Upload to Shopify: Use the “URL Redirects” import in Shopify Admin > Online Store > Navigation.
Pro Tip: Do not forget your image URLs. If you rank for image search, those file paths change too. Consider using a dedicated WooCommerce to Shopify Migration Service that specifically handles media asset re-mapping.
Product Data Transfer: The “Ghost” Inventory
You might see your product count match (e.g., 500 products in export, 500 in import), but the fidelity of that data is often compromised.
What Actually Breaks
- Variants: WooCommerce handles variants (Size, Color) as child-posts in the database. Shopify handles them as options. Complex variations often get flattened or exploded into separate products.
- Descriptions: Shortcodes (
[vcrow],) used in WooCommerce descriptions will render as broken text garbage in Shopify. - Metafields: Custom fields created with plugins like ACF (Advanced Custom Fields) do not have a native home in Shopify standard CSV imports.
The Fix: Data Sanitization
Before you import a single file, sanitize your description HTML. Strip out shortcodes. For extra metadata, you will need to utilize Shopify Metaobjects or Metafields.
Validation Checklist:
- [ ] Check 5 complex variable products (do they have the right SKUs?)
- [ ] Verify HTML descriptions (are there leftover shortcodes?)
- [ ] Check weight and dimensions (often default to 0 or kg/lb mismatches)
Customer Accounts & Password Encryption
This is the shocker for most merchants: You cannot migrate customer passwords.
The Technical Wall
WooCommerce hashes passwords using MD5 or stronger WordPress salts. Shopify uses its own proprietary hashing. You cannot copy-paste encrypted strings from one database to another and expect them to work.
The User Experience Crash
Your loyal customers try to log in to track their order on the new site using their saved credentials. It fails. They try again. It fails. They assume you’ve deleted their account or, worse, that you’ve been hacked. Support tickets spike by 400%.
The Solution: The “Activate Your Account” Strategy
You must treat this as a marketing campaign, not an IT ticket.
- Migrate the Customer Records: Import names, emails, and address books.
- Tag Them: Add a tag like
migratedcustomerin Shopify. - Send Invites: Use an email marketing tool (Klaviyo/Omnisend) or Shopify’s bulk inviter to send a branded email: “Welcome to our new home. For security, please reactivate your account and set a new password.”
Payment Gateways and Historical Subscriptions
If you run a subscription model using WooCommerce Subscriptions, you are entering the most dangerous phase of migration.
The Disconnect
Payment tokens (the encrypted keys that allow you to charge a card without seeing the number) are stored with your gateway (Stripe, PayPal, Authorize.net). However, the link between that token and the specific subscription ID in WooCommerce is often broken when moving to Shopify.
Shopify Subscription APIs are robust but different. You cannot simply “import” active recurring billing. In many cases, customers must re-enter their payment details, causing a massive churn event.
Mitigation
- Use an app like Recharge or Skio that has specialized specialized migration teams.
- Run a “legacy” transition where old subscriptions finish on the old system while new ones start on Shopify (messy, but safe).
Designing Your Migration Strategy with a Partner
Navigating the complexities of data fidelity, SEO mapping, and subscription logic requires more than just a CSV uploader—it requires execution experience. Book a discovery call with We Are Presta to discuss how our Startup Studio can manage your re-platforming, ensuring you migrate from WooCommerce to Shopify with no downtime while maximizing ROI and preserving your hard-earned SEO rankings.
The “Plugin” Functionality Gap
WooCommerce is a Lego set; you can build anything if you find the right block (plugin). Shopify is a walled garden.
What You Lose
- Specific SEO Tweaks: Yoast SEO on WordPress allows granular control that technically doesn’t exist 1:1 in Shopify native (though apps help).
- Custom Checkout Fields: Unless you are on Shopify Plus, the checkout is locked down. You cannot easily add “Date of Birth” or “Delivery Instructions” fields without specific UI extensions.
The Audit
Create a feature inventory. Do not just list plugins; list *what they do*.
- Plugin: YITH Wishlist -> Function: Allow users to save items. -> Shopify Equivalent: Wishlist Plus.
If you rely on a hyper-specific customization (e.g., “users can upload a PDF and then crop it before buying”), verify that a Shopify app exists *before* you migrate.
Order History and Analytical Continuity
Marketing directors hate migrations because “Year-over-Year” reporting breaks.
The Breakage
Imported orders in Shopify are often treated as “Archiived” or “Legacy”. They may not attribute to the correct sales channel or marketing source (UTM parameters are often lost). Your “Best Selling Products” report might reset to zero.
The Strategic View
Accept that your in-platform analytics will have a “Day Zero”. Use an external source of truth like Google Analytics 4 (GA4) or a BI tool to stitch together the data pre- and post-migration. Ensure your Shopify SEO Agency sets up GA4 tracking *immediately* upon launch to prevent data gaps.
Email Deliverability and Domain Reputation
You moved the site, but did you move the DNS records for your emails?
The Trap
Shopify sends transactional emails (Order Confirmed, Shipped) on your behalf. If you don’t continually validate your SPF and DKIM records in your DNS settings (`CNAME` records), Gmail and Outlook will mark your new store’s receipts as Spam.
Validation
- SPF: Include Shopify in your SPF record (
include:shops.shopify.com). - DKIM: Generate the CNAME records in Shopify Admin > Settings > Notifications and add them to your domain provider (GoDaddy, Namecheap, etc.).
Measuring Success: The Post-Migration KPI Framework
How do you know if the migration was a success? It’s not just “the site is up.” You need to track specific metrics for the first 90 days.
30-Day Stabilization Phase
- 404 Error Rate: Monitor in Google Search Console daily. Target: < 1%.
- Customer Service Volume: Track “login issue” tickets. Target: Decline week-over-week.
60-Day Optimization Phase
- Conversion Rate: Compare vs. WooCommerce average. Ideally, Shopify’s optimized checkout should boost this by 10-15%.
- Page Speed: Core Web Vitals should show all green (LCP < 2.5s).
90-Day Growth Phase
- Organic Traffic: Should return to pre-migration levels or exceed them.
- AOV (Average Order Value): Leverage Shopify’s upsell apps to drive this up.
Frequently Asked Questions
Will I lose my SEO rankings when acting on a WooCommerce to Shopify migration?
Not if you do it correctly. The primary cause of ranking loss is broken links (404s). If you implement a comprehensive 301 redirect map for every product, category, and blog post, Google transfers the authority to the new URL. Rankings may fluctuate for 2-4 weeks but should stabilize if the content remains consistent.
Can I transfer my WooCommerce theme to Shopify?
No. WooCommerce themes are PHP/HTML based. Shopify uses Liquid. They are incompatible technologies. You will need to rebuild your design using a Shopify 2.0 theme. This is actually a benefit, allowing you to modernize your UX/UI during the transition.
How long does a migration typically take?
For a simple store (under 100 SKUs), it can take 1-2 weeks. For complex stores with thousands of SKUs, customer data, and subscriptions, a professional migration project typically takes 4-8 weeks to allow for design, data testing, and QA.
Does Shopify cost more than WooCommerce?
On the surface, yes (monthly subscription vs. free plugin). However, when you factor in high-performance hosting, security plugins, developer maintenance hours, and potential downtime costs of WooCommerce, Shopify often has a lower Total Cost of Ownership (TCO) for scaling brands.
Can I migrate my blog posts?
Yes, you can import blog posts, but be careful with formatting. Images embedded in WooCommerce posts often link to the old WordPress media library. You need to ensure these images are downloaded and re-uploaded to Shopify’s CDN, or they will break when you cancel your old hosting.
What happens to my email accounts?
Shopify does not host email (e.g., `[email protected]`). You generally keep your email hosting where it is (Google Workspace, Outlook, Zoho) and just point the A-record to Shopify for the website traffic. Your email service remains uninterrupted if you don’t mess with the MX records.
