Biggest technical SEO problems on Shopify stores

Most Shopify stores don’t see rankings not because of weak content or poor design but because of technical SEO issues. You can  install a fast theme, add great products, and create well-written content and still see no significant ranking improvements.

Although some issues stem from Shopify’s limitations, many of them depend on how you set up and maintain your store. When auditing stores, we’ve seen merchants overlook essential steps, like submitting a sitemap to Google or using structured data.

In this guide, we break down the most common technical SEO problems we encounter on Shopify stores and show you how to fix them to improve rankings.

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Common technical SEO issues and solutions

We’ve been auditing Shopify stores for years now, and we keep noticing the same technical SEO problems. Some of them are minor drawbacks of Shopify itself, but many depend on how you set up your store. Here are the patterns we repeatedly see in SEO audits:

1. Duplicate content

In most Shopify store audits, duplicate URLs are some of the most common SEO problems we find. Shopify is known for duplicate content issues for both product and category pages, which can dilute ranking signals and confuse search engines about which version to rank.

For example, you can access product pages directly or through collection pages:

storename.com/products/product-title or through collection pages

or

storename.com/collection/collection-name/products/product-name.

The same goes for collection pages, since storename.com/collections/all would show the same content as storename.com/collections/all?page=1.

In many cases, Shopify automatically adds canonical tags to tell search engines which page version to prioritize. However, it may not always be the case.

Solution:

You can fix duplicate content issues by editing code using this “How to Fix Shopify Duplicate Content” guide. If you don’t have experience with coding, we highly recommend hiring a developer experienced with Shopify to do it for you.

2. Poor internal linking structure

When sites have a weak internal linking structure, search engines can have a hard time finding and prioritizing all important pages. So, certain products or other pages may end up not being ranked.

A common issue in Shopify stores is crawl depth, which refers to how many clicks it takes to reach a specific page from the homepage. Some merchants put important pages 4 or even more clicks away from the homepage. Also, store owners sometimes leave behind orphan pages on their site, which are pages that have no internal links pointing to them.

Solution:

Review your site structure and internal linking strategies to make it clear and organized. Here are the best practices to follow:

• Create a clear site structure with navigation menus and collections.
• Link to important products from high-traffic pages, like the homepage
• Use contextual links in your content, whether it’s collection descriptions or blog posts.
• Make sure important pages are accessible within 2-3 clicks from the homepage.
• Regularly audit your site for any orphan pages.

3. Collection pages with thin content

When auditing Shopify stores, we often notice that merchants overlook collection page content. Collection pages that are filled with products but don’t have any descriptions may struggle to rank.

That’s because collection pages without content only include the category name, which is likely a short-tail and high-intent keyword. So, search engines like Google may not have enough context to rank your page higher than competitors.

If you’re writing content for collection pages, just make sure it provides value to the user, is optimized for keywords, and clearly explains what the category offers.

Solution:

Take the time to write unique collection page descriptions for each collection page. It doesn’t have to be long; even a single paragraph can be enough.

For example, IKEA categorizes its products by rooms, writing unique descriptions and adding useful internal links.

When you go through the sub-collections, the category descriptions become shorter, but they’re still there. Each of them is unique and mentions important details to know.

4. Tag page indexing

Shopify generates tag-based URLs for filtered collections, such as /collections/dresses/size-6, which is considered low-value content. If they get indexed, it results in duplicate content, which dilutes ranking signals across similar pages.

Solution:

Shopify doesn’t have an easy way to manage page indexing, so you can only update your robots.txt file through code to disallow crawling tag-based URLs.

A single mistake can break your website’s layout, so we highly advise creating a backup and hiring a professional to deal with code.

5. Slow page load times (unoptimized images, unused apps)

Google has stated that page speed is an important ranking factor on both desktop and mobile devices, so it can be harder to rank if your page is extra slow.

Shopify handles the back-end speed optimizations, such as hosting. However, speed can still become slow over time as you install apps and grow your store.

Solution:

To speed up your Shopify store, run your website through PageSpeed Insights to know what exactly you should improve. Here are the main practices you should follow:

• Reduce app bloat. Each app you install on your website adds a new script, which slows down your store. Most fast Shopify stores we’ve audited keep between 2 and 5 all-in-one apps at most, but what matters is that you keep only the necessary tools.
• Compress images. Images can take a large portion of your page. According to a study by Almanac, images make up around 35-37% of total page weight. So, use free online compression tools or Shopify apps for image optimization to reduce their size.
• Enable lazy loading. PageSpeed Insights often gives you the “Defer offscreen images” insight, which means enabling lazy loading. It’s a technique where a web page delays the loading of non-essential resources so the page load time stays fast.
• Minify CSS and JavaScript files. Developers often leave unnecessary characters, comments, or spaces, making the file size bigger and slowing down your store. Use online minifiers or Shopify apps that offer minification to reduce your file size.

6. Basic structured data

Structured data doesn’t directly affect rankings, but it can help improve your site’s visibility in search results. It can also influence how Large Language Models (LLMs) understand your content, potentially affecting how your site appears in AI-generated answers.

Structured data gives context to search engines about your store and its content. It can include such information as pricing, availability, product details, or shipping policy.

When you install a theme on Shopify, it adds some structured data automatically, but it’s usually very minimal. If, for example, there’s no Product schema, you can miss out on appearing in rich snippets or rich results.

Solution:

You can easily check if your Shopify store has schema and its types by using a free online schema checker or checking it through the TinyIMG Chrome extension.

There are two ways you can add structured data to your website – manually through code or automatically with a Shopify app that offers automatic JSON-LD setup.

If you choose the automatic option, pick an app that offers comprehensive SEO optimization instead of a single feature.

For the manual method, we’d recommend getting a developer. But if you know how to code or want to learn, you can learn more about different schema types on the schema.org website.

7. Submitting a sitemap

A sitemap is a file with information about your website’s pages, files, and relationships between them. Its purpose is to help search engines like Google discover and understand your store’s structure.

While Shopify generates sitemaps automatically, some beginner merchants think it’s enough for indexing. But without actually submitting a sitemap, Google may take much longer to discover and crawl your pages.

Solution:

Submit your sitemap to Google Search Console (GSC), so Google crawls your site regularly. You can find your sitemap by adding /sitemap.xml to your domain, like example.com/sitemap.xml.

To submit your sitemap, follow these steps:

1. Create a GSC account and verify your account per instructions.
2. Open GSC and go to Indexing > Sitemaps.
3. Add “sitemap.xml” in the “Add a new sitemap” section.
4. Press Submit.

Just make sure to check the indexing status and fix any crawl errors if GSC shows it.

8. Strict URL structure

Shopify doesn’t give enough flexibility when it comes to URL structure, so you’re stuck with a fixed structure. For example, a clean URL of a product page can look like this:

example.com/mirrors/oval-mirror-with-led-lightning

On Shopify, it would look like this:

example.com/collections/mirrors/products/oval-mirror-with-led-lightning

Solution:

The fact that you can’t remove the core folders from the URL has been a well-known issue on Shopify for years. It may be a limitation when you prefer short and clear URLs, but SEO rankings won’t be affected if you build a logical site structure.

So, work with what you have and optimize the URL handles:

• Keep URL handles short and clear, including the main keyword
• Separate words in the URL handle using hyphens
• Try to avoid unnecessary numbers or duplication

Make sure you also use internal linking effectively, like creating organized navigation menus and adding breadcrumbs.

9. Poor SEO metadata

SEO metadata, or meta titles and meta descriptions, are what users first see in search results about a web page. If your SEO metadata isn’t enticing, users won’t click on your site, resulting in lower click-through rates.

Despite SEO expert tips, many merchants still use generic or duplicate titles and descriptions. We still notice websites missing meta descriptions or adding ones that exceed the recommended character limit.

Solution:

To make sure your click-through rates don’t suffer, follow the best meta title and meta description practices:

• Write unique meta titles for each page and include the main keyword.
• Meta titles should be under 60 characters, while meta descriptions don’t get cut off under 160 characters.
• Meta descriptions should describe what your page is about.
• Add a call to action (CTA) to meta descriptions to invite users to click.

You can drop your website URL into this free metadata checker to see if your titles and descriptions follow recommended practices.

10. Lack of content strategy

While content should fall under the on-page SEO category, technical SEO wouldn’t work on a website without content. We’ve found that many Shopify merchants overlook the importance of content, so they miss out on organic traffic that would help people learn about their brand.

In some cases, merchants do write content, but it doesn’t rank because they don’t perform keyword research in advance.

Solution:

Start writing blog posts to get traffic and build up brand authority. It’s both an effective SEO and AEO (Answer Engine Optimization) strategy to gain exposure. Here are the main things to note about SEO blog creation:

• Perform keyword research with SEO tools like Ahrefs or Semrush to analyze which keywords you should focus on.
• Check what your competitors are writing about.
• Focus on long-tail keywords because they’re easier to rank for.
• Show your expertise through blog posts and build authority.
• Write blog posts about your products to answer common questions.
• Add internal links to relevant products naturally.

Final thoughts

Although Shopify is a powerful platform for eCommerce, it comes with technical SEO limitations to be aware of. There are many Shopify stores in different niches that rank at the top of Search Engine Results Pages (SERP), so you have to know how to navigate the issues.

We’ve also noticed common technical SEO tasks that merchants overlook, especially as their store grows. Something as simple as submitting a sitemap to Google, optimizing your site speed, or adding structured data can help gain more visibility.

However, technical SEO isn’t a one-time task, so regularly audit your website for any potential issues as your store grows.

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About the author

Kristina Jaruseviciute

Kristina is a Content Lead at TinyIMG responsible for informing and educating readers on all things Shopify-related. She covers a broad range of topics around SEO, AI visibility, website performance, and conversion rates to help merchants stand out in a competitive landscape.