7 Core Technical SEO Challenges For Shopify Websites & How To Fix Them

There's no doubt Shopify is a powerful eCommerce platform, but it comes with its own set of technical SEO challenges that website owners must address to improve search rankings and user experience.

Many of these limitations are inherent to a Shopify website's structure, making it essential to understand and work within these constraints to ensure we achieve the best results.

I’m very lucky to work with Shopify developers at blubolt who understand these challenges, find time to listen and take on board my knowledge and thoughts, specifically in technical SEO. Together, we have explored some of the common Shopify SEO challenges and how to mitigate them.

1. URL structure & duplicate content issues.

One of the biggest SEO pitfalls in Shopify is its default URL structure. It’s not one that I’ve come across at blubolt yet, thanks to our knowledgeable development team, but still an important point to make. Shopify generates multiple URLs for the same product when it is assigned to multiple collections, which can lead to duplicate content issues.

Common Issues.

• Products can appear under multiple collection-based URLs, creating duplicate pages.

• URLs often contain unnecessary elements that make them long and cluttered.

• Shopify’s default structure limits the ability to create an SEO-friendly hierarchy.

Solutions.

• Customise URLs to use only the product slug instead of collection-based paths.

• Implement canonical tags on product pages to indicate the preferred URL to search engines.

• Modify Shopify’s liquid code to remove the within collection text that forces URL duplication.

• Make use of Tags where we have broad collections such as ‘New In’; it's possible to extend these via tags to produce clean URLs like ‘/new/womens’ and ‘/new/mens’

2. Limited control over site structure.

Due to its predefined structure, Shopify makes it difficult to create an intuitive category and subcategory relationship that we would expect for SEO and improved top-down, bottom-up navigation.

Challenges.

• Shopify lacks true parent-child category functionality, leading to poor page and category organisation.

• Breadcrumb navigation, as a result, is naturally shallow, limiting internal linking capability.

• Shopify collections don’t allow for proper hierarchical subcategories.

Thoughts on solutions.

• Use smart internal linking to improve navigation and category relationships.

• Optimise collections with clear, keyword-rich titles and descriptions.

• Implement breadcrumb schema markup to help Google understand the site structure better.

3. Robots.txt customisation confusion.

Shopify does not present users with a simple method to directly edit the robots.txt file or fine-tune what’s crawled and what’s not; for larger eCommerce stores, this immediately limits control for internal teams with limited knowledge over what pages are crawled and indexed by search engines.

Why this matters.

• Crawlers may waste time on unimportant pages, such as filtered collections that can often find themselves hidden in sitemaps.

• Shopify’s default robots.txt settings may also block useful content from being indexed.

Best practice.

• Gain back control by creating a robots.txt file within your Shopify Theme. Once in place, keep important pages, such as collections, products, and blogs, accessible to search engines.

• Restrict low-value pages such as checkout, cart, and admin pages to avoid wasting crawl budget.

• Remember to monitor and test changes in the Google Search Console to ensure key pages remain indexable.

4. Page speed & performance issues.

Page speed is a direct ranking factor for Google, made apparent through the adoption of Core Vitals, but Shopify websites often suffer from slow loading times due to unoptimised themes and, in most cases, excessive app usage.

Common causes of slow Shopify pages.

• Third-party apps have injected unnecessary or uncompressed JavaScript and CSS.

• We want to give the best representation of our products and brands but remember, large image sizes lead to heavy page loads.

• Excessive reliance on Shopify’s default scripts, slowing down rendering.

How to improve Shopify site speed.

• Use Shopify’s native image compression and adopt WebP formats for faster load times.

• Minimise the number of apps, carry out regular housekeeping checks, and remove those that add unnecessary scripts.

• If you don’t already, enable lazy loading for images and videos to improve performance.

• A CDN (Content Delivery Network) such as Cloudflare can be used to serve static files more efficiently.

5. Weak meta tags & descriptions.

Many Shopify websites suffer from auto-generated title tags and meta descriptions, leading to duplicate or missing metadata, which can negatively impact organic search performance.

Common issues.

• Shopify dynamically generates meta descriptions and can often truncate them improperly.

• Product pages almost always lack unique, keyword-rich title tags.

• Meta descriptions are often poor and don’t always align with search intent.

Solutions.

• Invest in a solid keyword research and tracking tool.

• Manually optimise title tags and descriptions for high-value pages.

• I know I said remove apps, but when it comes to Shopify SEO, they can help manage metadata and plug gaps at scale.

• We should not forget to keep an eye on performance by conducting regular site audits to ensure all pages have properly formatted metadata.

6. Missing schema markup.

Rich snippets or structured data help search engines crawl and better understand page content, but Shopify does not include rich schema markup by default, which makes it harder for search engines to extract product information, potentially limiting your presence in search results.

Why schema markup matters.

• It helps products appear in rich results, such as Google Shopping.

• It aids artificial intelligence (AI) in finding responses to common questions and surfacing information in an AI-generated summary.

• It allows crawlers to understand content types like FAQs, Articles and Reviews.

• Enhances click-through rates (CTR) in SERPs.

How to fix it.

• Add schema markup manually in Shopify’s theme files.

• I know, but where technical literacy can escape us, it's possible to use a Shopify SEO app to automate structured data markup for products.

7. Duplicate content from filtered pages & pagination.

I mentioned it briefly above, but Shopify can and will create duplicate content when users apply filters or browse paginated collections, potentially creating tens, sometimes even hundreds, of essentially duplicate pages.

Common problems.

• Filtered pages generate dynamic URLs that Google may index as duplicate content.

• Pagination may cause canonical conflicts and dilute ranking.

Solutions.

• It's really important to implement canonical tags to direct search engines to the main product or category page; this is also true of localised products to ensure we’re not duplicating content across similar language markets.

• An option is to use AJAX-based filtering to keep filter-based pages from generating new URLs, of course, it's cleaner for SEO but limits the possibility of shoppers sharing filtered categories with friends.

Final thoughts on technical SEO.

Shopify is undoubtedly a powerful platform for eCommerce, but as I’ve outlined above - it has built-in SEO limitations that eCommerce teams and agencies must navigate. Addressing these all-too-common technical SEO challenges, from fixing duplicate content issues to improving site structure and page speed, will lead to better rankings and a stronger presence in Organic Search Results Pages (SERPs).

Be proactive, consistently regularly checking and managing these constraints; you will quickly be able to enhance the user experience and drive more traffic through to conversion.

If you’re looking to improve your eCommerce SEO, our expert team at blubolt can help! Browse our SEO eCommerce services, find inspiration from our work, and get in touch to discuss your requirements today.