Introduction
Migrating your website to Shopify is a smart move for scalability, performance, and ease of management. But amid the excitement of a new design, modern functionality, and improved user experience, many site owners overlook one crucial element: SEO. A poorly executed migration can cost you years of organic search value—leading to lost rankings, traffic, and revenue.
In this blog, we’ll break down the hidden SEO risks during a Shopify migration and how to avoid them so you can transition smoothly without compromising your online visibility.
Ignoring Existing SEO Structure
One of the most common mistakes during migration is not preserving the original SEO structure. Your URLs, meta tags, internal linking, and keyword-targeted content have been helping your website rank—ignore them at your peril.
How to Avoid It:
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Use tools like Screaming Frog or Ahrefs to crawl your existing site and document all important pages, URLs, and metadata.
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Maintain your most valuable URLs or set up proper 301 redirects (more on this below).
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Copy over title tags, meta descriptions, headers, and alt text.
Broken or Incorrect Redirects
When URLs change, setting up proper redirects is non-negotiable. Otherwise, users and search engines hit 404 errors, which lead to poor UX and plummeting rankings.
How to Avoid It:
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Create a complete redirect map: Match every old URL to its new equivalent.
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Use Shopify’s built-in 301 redirect tool or apps like “Easy Redirects.”
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Double-check redirects with tools like Screaming Frog or Google Search Console after launch.
Content Loss or Rewriting Without SEO Review
It’s tempting to rewrite or shorten content during migration to match a cleaner look—but doing so without an SEO lens can remove critical keywords or topical relevance.
How to Avoid It:
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Audit top-performing pages (via Google Analytics or Search Console) and ensure their content is preserved or strategically enhanced.
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Retain key H1s, keyword phrases, and FAQ-rich sections.
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If rewriting, keep old pages live until new ones are indexed and performing.
Not Handling Canonical Tags Correctly
Canonical tags signal to Google which version of a page is the master copy. If these aren’t transferred correctly or point to the wrong URLs, your SEO can suffer from duplicate content confusion.
How to Avoid It:
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Audit your current site’s canonical structure.
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Implement correct canonical tags in Shopify using the “Edit Code” section of your theme or with help from SEO apps.
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Avoid multiple pages competing for the same keyword unless purposefully planned.
Forgetting XML Sitemap and Robots.txt Optimization
When switching platforms, your XML sitemap and robots.txt file may change—potentially blocking search engines from crawling your site or missing important pages.
How to Avoid It:
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Generate a new XML sitemap in Shopify and submit it to Google Search Console.
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Customize your robots.txt in Shopify to allow access to critical resources (like images, JS, CSS).
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Test crawlability using tools like the URL Inspection Tool.
Ignoring Structured Data and Schema Markup
Schema helps search engines understand your site better, leading to enhanced visibility like rich snippets. Unfortunately, the schema often gets stripped out during migration.
How to Avoid It:
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Audit current schema types: Product, Breadcrumb, Article, Review, etc.
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Re-implement schema via Shopify’s theme code or with apps like “JSON-LD for SEO.”
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Test schema with Google’s Rich Results Test.
Not Setting Up Google Search Console and Analytics
After migration, failing to re-verify your domain and track data can delay performance monitoring—keeping you blind to emerging issues.
How to Avoid It:
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Re-verify your new Shopify site with Google Search Console and Bing Webmaster Tools.
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Ensure Google Analytics is properly installed and linked to your new site.
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Track performance weekly post-migration to catch ranking or indexing issues early.
Forgetting Image Optimization
Large, uncompressed images or missing alt attributes can slow down your new Shopify site and hurt your SEO.
How to Avoid It:
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Compress images using Shopify’s built-in optimizer or third-party apps like TinyIMG.
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Add descriptive alt text to all product and banner images.
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Ensure proper filenames that include target keywords where relevant.
Conclusion
Migrating to Shopify can be a massive upgrade for your eCommerce business—but only if executed with SEO in mind. The hidden SEO risks during Shopify migration are real, but with planning, audits, and the right tools, they are entirely avoidable.
Start with a comprehensive SEO audit of your current site, map out your migration path with redirects and metadata in place, and use this move as an opportunity to build a stronger foundation. A well-migrated site can preserve your current rankings and even improve them in the long run.