Shopify SEO Issues: A 2025 Technical SEO Checklist

Shopify remains one of the most popular e-commerce platforms in the world, thanks to its ease of use and scalability. However, it’s not without its SEO challenges.

Whether you’re an in-house SEO, agency-side consultant, or an ambitious store owner, understanding and addressing technical SEO issues with Shopify is critical for long-term organic growth.

This checklist-style guide will walk you through the most common Shopify SEO issues in 2025 – from crawl inefficiencies to schema errors – and provide expert insights on how to fix them.

Introduction: Why Technical SEO Matters in Shopify

Shopify makes launching an online store simple, but it comes with SEO quirks that can quietly cap your organic growth. Fixed URL structures and reliance on third-party apps are two of the biggest limitations – and if left unchecked, they can hold back your best-selling products from ranking.

That’s why technical SEO isn’t optional in 2025. Search engines and large language models now expect sites to be fast, crawlable, and well-structured, and failing to meet those standards means losing visibility to competitors who do.

This checklist is built to help you spot the most common Shopify SEO problems quickly and fix them efficiently, giving your store the strongest possible foundation to rank higher and convert more customers.

1. Audit Default URL Structures

Shopify’s default URLs for products and collections include /products/ and /collections/ in the path. While straightforward, this setup can cause SEO headaches.

One common issue is duplicate content from URLs like /collections/*/products/*, which show the same product but under different collection paths. Search engines may get confused, splitting ranking signals across multiple URLs.

To fix this, use canonical tags properly to point all duplicates back to the main product URL. Also, review your internal linking to ensure all internal links point to indexed versions of URLs.

Keeping your URL structure signals clean and consistent helps search engines crawl and index your site efficiently, improving your overall Shopify SEO health.

2. Identify Internal Linking to No-Index Pages 

A common Shopify SEO issue is internal links pointing to the wrong product URL format. By default, Shopify allows products to be accessed through multiple paths – for example:

• Correct:/products/product-name
• Problematic:/collections/collection-name/products/product-name

Those collection-based product URLs are typically set to no-index. If your internal links point there instead of the clean product URL, search engines waste crawl budget on pages that won’t rank – diluting your site’s overall SEO performance. Cleaning up these links ensures crawlers focus on the URLs that actually matter for visibility and ranking.

3. Resolve Faceted Navigation Crawl Issues

Shopify stores often use filters to help shoppers narrow down products by size, colour, price, and more. However, these filters add parameters to URLs, creating countless variations of the same page.

The Problem with Filtered URLs

• Search engines see these as separate URLs.
• This leads to duplicate content.
• Crawl budget is wasted.
• Ranking signals become diluted.
• Crawlers can become confused.

How to Fix Faceted Navigation Issues

• Identify Filter URLs Being Crawled
  Start by determining which filter URLs search engines are accessing.
• Use robots.txt Rules
  Block crawling of unnecessary parameter combinations to prevent search engines from indexing duplicate pages.
• Set Canonical Tags
  Apply canonical tags on filtered pages pointing to the main category URL. This signals to search engines which version to prioritise.

Benefits of Proper Faceted Navigation Management

• Prevents index bloat.
• Keeps your SEO clean and focused.
• Boosts your Shopify store’s organic performance.

4. Review Theme and App-Generated Schema Markup

Shopify themes and apps often add schema markup automatically to boost rich results, but this can backfire if not managed properly. Common issues include duplicate schema types, conflicting data, or incomplete markup that confuses search engines.

For example, multiple JSON-LD scripts might describe the same product differently, diluting SEO value or triggering errors in Google’s Rich Results Test. To fix this, audit your site’s structured data regularly. Use Google’s Rich Results Test to spot errors or duplicates. Where possible, customise or remove redundant schema from apps or themes, and consider manually editing JSON-LD markup to ensure accuracy and consistency. This keeps your structured data clean and effective for SEO for ecommerce.

5. Evaluate Site Speed and Core Web Vitals

Shopify stores often rely heavily on apps and third-party scripts, which can drag down site speed. Slow loading times hurt user experience and can tank your rankings since Google’s Core Web Vitals (CWV) are now a major ranking factor. CWV focuses on loading performance, interactivity, and visual stability – all critical for keeping shoppers happy and engaged.

To fix this, start by auditing which apps you really need. Remove or replace those that add unnecessary bloat. Next, defer or asynchronously load non-essential scripts to prevent them from blocking page rendering. Shopify’s built-in image optimisation tools are a must-use-make sure all images are compressed and served in modern formats like WebP. Keeping your store lean and fast is key to winning in 2025’s SEO game.

6. Check for Pagination and Infinite Scroll Issues

Shopify themes often use infinite scroll to load products continuously, which looks great but can cause SEO headaches. Search engines may struggle to crawl and index all your products properly if there’s no clear pagination structure. Without crawlable pages, ranking signals get diluted, and some products might never appear in search results.

To fix this, ensure your store uses crawlable pagination with rel=”next” and rel=”prev” tags. These tags help search engines understand the sequence of pages. If infinite scroll is a must, implement it so that it progressively loads crawlable URLs, or provide alternative paginated links that users and bots can access. This balance keeps your UX smooth while maintaining SEO health.

7. Audit International SEO Setup

Shopify’s built-in international SEO options are limited, which can cause issues if you’re targeting multiple countries or languages. Common problems include:

• Missing or incorrect hreflang tags
• Relying on Shopify’s default country-specific domains without proper geotargeting

These issues can confuse search engines and dilute your rankings.

How to Fix These Issues

To improve your international SEO setup, consider the following steps:

• Use subdirectories (like example.com/uk/) or subdomains (uk.example.com) for different regions
• Implement accurate hreflang tags pointing to each version of your site
• Set up geotargeting in Google Search Console to signal the intended audience

This approach helps Google serve the right content to the right users and avoids duplicate content penalties.

8. Monitor Indexation via Search Console

Keeping a close eye on what Google indexes from your Shopify store is crucial. Even with Shopify’s built-in SEO features, unwanted pages can slip into the index, which may hurt your rankings and waste your crawl budget.

Common Issues to Watch For

• Outdated product variants
• Filtered collections
• No-indexed pages that are still indexed

How to Monitor Your Indexation

Regularly check Google Search Console to see which URLs are indexed and identify any surprises. Use the Coverage report to:

• Spot errors
• Find excluded pages

Actions to Take for Unwanted Pages

If you find pages that shouldn’t be indexed, take the following steps:

• Update your robots.txt file
• Add noindex tags to the pages
• Remove the pages from your sitemap

Keeping Google Updated

Submitting updated sitemaps through Search Console helps Google crawl your site efficiently and reflect your SEO fixes faster.

9. Optimise XML Sitemaps

Shopify automatically generates XML sitemaps to help search engines find your pages. But these sitemaps can sometimes include pages that don’t need indexing, like no-indexed or duplicate content. This can confuse search engines and waste crawl budget. To keep things tight, regularly audit your sitemap files. Remove or block unnecessary URLs by using noindex tags on those pages or disallowing them in your robots.txt file. This helps search engines focus on your most important pages, improving your site’s SEO performance without extra hassle.

Conclusion: Staying Ahead of Shopify SEO Challenges

SEO for Shopify isn’t set-and-forget. Technical issues can quietly drag your rankings down if left unchecked. Regular audits help you spot problems early and keep your store running smoothly in search results. Stay on top of platform updates and adapt your strategy as Shopify evolves. Even with its limits, Shopify can deliver strong SEO performance when you tackle these challenges head-on and keep your site lean, clean, and crawl-friendly. Don’t settle-make SEO a continuous part of your store’s growth plan.

Need help from the Shopify SEO Experts?

If your store is struggling with duplicate URLs, crawl budget waste, or product pages that never seem to rank, you’re not alone – these are some of the most common (and costly) Shopify SEO pitfalls.

The good news? They’re fixable. Our team of Shopify SEO experts specialises in untangling Shopify’s quirks and turning your site into a clean, scalable ecommerce SEO engine that drives sales. Need some help? Book a free consultation today and get a clear action plan to unlock your Shopify store’s organic growth.