Shopify SEO Audit Guide: How to Audit Your Shopify Store for SEO Issues

Why You Need a Shopify SEO Audit

An SEO audit is a systematic evaluation of every factor that influences how search engines discover, crawl, index, and rank your Shopify store. Without one, you are making optimization decisions based on assumptions rather than data. You might be spending hours rewriting product descriptions while a single misconfigured canonical tag is preventing Google from indexing half your catalog.

The typical Shopify store accumulates SEO issues over time. Theme updates introduce new HTML structure problems. Apps inject scripts that slow down pages. URL handles get changed without setting up redirects. Products go out of stock and create soft 404 patterns. These issues rarely cause a sudden traffic drop—they erode performance gradually, making them difficult to spot without a structured audit process.

What a Shopify SEO audit reveals

A thorough audit covers four main dimensions:

• Technical health — Crawl errors, broken links, redirect chains, page speed issues, Core Web Vitals failures, indexation gaps, and structured data errors that prevent search engines from properly processing your store.
• On-page optimization — Title tags, meta descriptions, heading structure, image alt text, internal linking patterns, and keyword targeting across product pages, collection pages, and content pages.
• Content quality — Thin content, duplicate descriptions, keyword cannibalization, content gaps relative to competitors, and opportunities to create new content that captures search demand.
• Off-page signals — Backlink profile health, toxic link identification, competitor link gap analysis, and domain authority trends that indicate your store's overall search credibility.

Technical SEO Audit

The technical audit is the foundation of your entire SEO review. If search engines cannot efficiently crawl and index your store, nothing else you optimize will matter. Start here and fix critical technical issues before moving to on-page or content analysis.

Crawling your Shopify store

Begin by running a full site crawl using Screaming Frog, Sitebulb, or a similar crawler. Configure the crawler to respect your robots.txt but also run a secondary crawl that ignores robots.txt so you can see what URLs exist that might be accidentally blocked. For Shopify stores, set the crawler to handle JavaScript rendering if possible—some Shopify themes and apps inject content via JavaScript that a basic HTML-only crawl will miss.

From your crawl data, extract and analyze these critical metrics:

• Response codes — Categorize all URLs by HTTP status code. Flag all 404 errors (broken pages), 301 and 302 redirects (check for redirect chains and loops), and 500 errors (server issues). On a healthy Shopify store, 90 percent or more of crawled URLs should return 200 status codes.
• Redirect chains — Identify URLs that redirect through two or more hops before reaching the final destination. Redirect chains waste crawl budget and dilute link equity. Common on Shopify stores that have changed URL handles multiple times without updating old redirects.
• Orphan pages — Find pages that exist in your sitemap or receive external links but have no internal links pointing to them. Orphan pages are difficult for Google to discover and are typically undervalued in rankings.
• Crawl depth — Check how many clicks it takes to reach each page from the homepage. Important product and collection pages should be reachable within 3 clicks. Pages buried 5 or more clicks deep rarely rank well.

Indexation analysis

Open Google Search Console and navigate to the Pages report (formerly Coverage). This shows you exactly how Google sees your indexation status. Pay attention to these categories:

• Indexed pages — Compare the number of indexed pages against the number of pages you want indexed. If you have 500 products and 50 collections but only 300 indexed pages, you have an indexation gap that needs investigation.
• Excluded pages — Review the reasons Google gives for excluding pages. Common Shopify exclusions include "Duplicate without user-selected canonical," "Crawled but not indexed," and "Page with redirect." Each exclusion reason requires a different fix.
• Not indexed: discovered but not crawled — If many pages fall into this category, it indicates crawl budget issues. Google knows these pages exist but does not consider them important enough to crawl. This is common with faceted navigation URLs and deep pagination pages on Shopify.

Page speed and Core Web Vitals

Test your key page templates using Google PageSpeed Insights: homepage, a product page, a collection page, and a blog post. Record both lab data (Lighthouse scores) and field data (real-user metrics from the Chrome User Experience Report). Focus on the three Core Web Vitals:

• Largest Contentful Paint (LCP) — Should be under 2.5 seconds. On Shopify, poor LCP is usually caused by unoptimized hero images, render-blocking app scripts, or slow theme JavaScript. Check if your main product image or hero banner is preloaded and properly sized.
• Interaction to Next Paint (INP) — Should be under 200 milliseconds. Shopify stores with many installed apps often have INP issues because each app adds JavaScript that competes for main thread time. Use Chrome DevTools Performance tab to identify long tasks during user interactions.
• Cumulative Layout Shift (CLS) — Should be under 0.1. Common CLS culprits on Shopify include images without explicit dimensions in theme templates, late-loading app widgets that push content down, and web font loading that causes text to reflow.

Broken links and redirect audit

Your crawl data will reveal broken internal links, but you should also check for broken external links. Internal broken links are typically caused by deleted products or collections where the internal links were not updated. On Shopify, this happens frequently when products go out of stock permanently and their pages are removed.

For redirects, audit the full redirect map in your Shopify admin under Settings > Navigation > URL Redirects. Look for redirect chains (old URL redirects to another old URL that redirects to the current URL), redirect loops, and redirects pointing to pages that no longer exist. Export the full redirect list and cross-reference it with your crawl data to identify gaps.

On-Page SEO Audit

On-page SEO is where most Shopify stores have the highest density of fixable issues. Because Shopify generates default values for many on-page elements, store owners often assume these defaults are sufficient. They are not. A systematic on-page audit identifies every page where title tags, meta descriptions, headings, and other on-page elements are missing, duplicated, or poorly optimized.

Title tag analysis

Export all title tags from your crawl data and analyze them for these issues:

• Missing titles — Pages with empty or missing title tags. Shopify auto-generates titles from the product or collection name plus your store name, but custom pages and some blog posts may have empty titles if not configured manually.
• Duplicate titles — Multiple pages with identical title tags. This is common when product variants create separate URLs, or when collection pages with filters generate unique URLs but share the parent collection's title.
• Titles that are too long or too short — Title tags should be between 50 and 60 characters. Titles that exceed 60 characters get truncated in search results. Titles under 30 characters miss opportunities to include keywords and compelling copy.
• Missing primary keyword — Each product and collection page should target a specific keyword that appears near the beginning of the title tag. Check that your titles include the term people actually search for, not just your internal product name or SKU.
• Branding format — Decide on a consistent title format. Most Shopify stores use "Product Name | Store Name" or "Product Name - Store Name." Ensure this format is applied consistently across all page types.

Meta description analysis

Meta descriptions do not directly influence rankings, but they significantly affect click-through rates from search results. A compelling meta description can be the difference between a searcher clicking your result or a competitor's.

• Missing descriptions — Shopify does not auto-generate meta descriptions for all page types. Check that every product, collection, page, and blog post has a custom meta description written in the "Search engine listing preview" section.
• Duplicate descriptions — Similar products often share nearly identical descriptions. Each page should have a unique meta description that differentiates it from similar pages on your own site.
• Length issues — Keep meta descriptions between 120 and 155 characters. Shorter descriptions waste SERP space. Longer ones get truncated and may cut off your call to action.
• Missing value proposition or CTA — Effective meta descriptions include a primary keyword, a clear benefit or differentiator, and a subtle call to action like "Shop now," "Free shipping," or "Compare prices."

Heading structure audit

Proper heading hierarchy helps both search engines and users understand the content structure of each page. Check your Shopify store for these heading issues:

• Multiple H1 tags — Each page should have exactly one H1 tag. Some Shopify themes incorrectly assign H1 to the store logo, promotional banners, or section titles in addition to the main page content heading.
• Missing H1 tags — Verify that product pages use the product title as H1, collection pages use the collection title, and blog posts use the post title. Some themes style these elements as headings visually but use div or span tags in the HTML.
• Skipped heading levels — Headings should follow a logical hierarchy: H1, then H2, then H3. Jumping from H1 to H4 or using H3 before H2 signals poor document structure to search engines.

Image optimization audit

Images are critical for ecommerce SEO, both for web search and Google Images traffic. Audit every product and collection page image for:

• Missing alt text — Every product image should have descriptive alt text that includes the product name and relevant attributes. Shopify makes it easy to add alt text in the product media section, but many store owners skip this step.
• Generic alt text — Alt text like "product image," "photo," or auto-generated filenames provide zero SEO value. Replace generic alt text with descriptive, keyword-appropriate text like "Women's leather crossbody bag in cognac brown - front view."
• File size — Large image files slow down page load times. Identify images over 200KB and compress them. Shopify automatically serves WebP format through its CDN, but starting with optimized source files yields better results.
• Missing width and height attributes — Images without explicit dimensions cause layout shifts as they load. Check your theme templates to ensure all image elements include width and height attributes or use CSS aspect-ratio.

Content Quality Audit

Content quality determines whether Google considers your pages worthy of ranking for competitive keywords. A content audit goes beyond checking for missing elements—it evaluates whether your content is substantive enough to compete in your market and comprehensive enough to satisfy search intent.

Product description analysis

Thin product descriptions are the single biggest content problem on Shopify stores. Export all your product descriptions and evaluate them against these criteria:

• Word count — Product descriptions under 100 words are almost certainly too thin. Aim for at least 250 to 300 words for every product, with more detailed descriptions for high-value or complex products. The top-ranking product pages in most ecommerce categories have 500 or more words of unique content.
• Uniqueness — If you are using manufacturer-supplied descriptions, you are competing with every other store using the same text. Google has no reason to rank your page over any of them. Rewrite every product description in your own voice with unique angles, use cases, and details that other stores do not provide.
• Keyword targeting — Check that each product description includes the primary keyword naturally in the first paragraph and uses related terms throughout. Avoid keyword stuffing—write for humans first, but ensure the language aligns with what people actually search for.
• Structure — Well-structured descriptions convert better and rank better. Use an opening paragraph that addresses the buyer's primary need, followed by bullet points for features and benefits, then a detailed specification section. This format helps both shoppers and search engines parse the content quickly.

Collection page content

Most Shopify stores leave collection pages as bare product grids with no descriptive content. This is a major missed opportunity. Collection pages can rank for high-volume category-level keywords, but only if they have enough unique content for Google to understand what the page is about.

Audit each collection page for descriptive content above or below the product grid. Each collection should have at least 150 to 300 words of unique, keyword-optimized text that describes what the collection contains, who it is for, and what differentiates your products from competitors. Add longer content sections below the product grid on your most important collection pages for additional topical depth.

Keyword cannibalization check

Keyword cannibalization occurs when multiple pages on your store target the same keyword, causing them to compete against each other in search results. This is common on Shopify stores where a collection page and a blog post both target the same term, or where similar products have overlapping keyword targets.

To identify cannibalization, export your Google Search Console data and look for queries where multiple URLs from your store appear. If two or more pages are competing for the same keyword and their rankings fluctuate, you have a cannibalization problem. The fix is to consolidate: choose one page as the primary target, optimize it thoroughly, and either differentiate the competing pages to target related but distinct keywords, or merge them and redirect the weaker page to the stronger one.

Content gap analysis

A content gap analysis reveals keywords your competitors rank for that you do not. Use Ahrefs or Semrush to compare your store's keyword profile against your top 3 to 5 competitors. Focus on keywords with high commercial intent—terms that indicate buying readiness like "best," "buy," "compare," and "review." These gaps represent direct revenue opportunities you can capture by creating new product pages, collection pages, or blog content.

Link Profile Analysis

Your backlink profile is one of the strongest ranking signals Google uses to evaluate your store's authority and trustworthiness. A link profile audit identifies both risks (toxic links that could trigger penalties) and opportunities (link-worthy assets and competitor link sources you can replicate).

Backlink health check

Pull your full backlink profile from Ahrefs, Semrush, or Moz and analyze it for these factors:

• Total referring domains — The number of unique domains linking to your store is more important than total backlink count. A store with 500 links from 200 domains is healthier than one with 5,000 links from 50 domains.
• Domain authority distribution — A natural link profile has links from a mix of high, medium, and low authority domains. If the majority of your links come from very low authority or spammy domains, it could signal a problem.
• Anchor text distribution — Check the anchor text used in links pointing to your store. A natural profile has mostly branded anchor text (your store name), followed by URL anchors, generic anchors ("click here," "learn more"), and a smaller percentage of keyword-rich anchors. If an unnaturally high percentage of your anchors are exact-match commercial keywords, it could trigger a Google penalty.
• Link velocity — Track how your backlink acquisition has trended over time. Sudden spikes followed by drops can indicate unnatural link building. Steady, gradual growth is the healthiest pattern.

Toxic link identification

Not all backlinks help your rankings. Some can actively harm them. Identify potentially toxic links by looking for links from:

• Domains with extremely low domain authority and no real content
• Link farms and Private Blog Networks (PBNs)
• Foreign language sites with no relevance to your market
• Sites with sitewide footer or sidebar links pointing to your store
• Comment spam and forum profile links

If you identify a significant number of toxic links, consider using Google's Disavow Tool to tell Google to ignore them. However, use the disavow tool cautiously—disavowing legitimate links can harm your rankings. Only disavow links that are clearly spammy and that you have attempted to remove through direct outreach first.

Internal linking audit

Internal links distribute authority throughout your store and help Google discover all your pages. Audit your internal linking structure for:

• Orphan pages — Pages with no internal links pointing to them. These are effectively invisible to Google unless they appear in your sitemap or have external backlinks.
• Link distribution — Check that your most important pages (high-revenue products, key collection pages) receive the most internal links. Many Shopify stores have flat internal linking where every product gets equal internal link equity regardless of importance.
• Anchor text — Internal link anchor text should be descriptive and keyword-relevant. Avoid generic anchors like "click here" or "view product." Use the product name or a descriptive phrase that includes your target keyword.
• Cross-linking between content and products — Blog posts should link to relevant products and collections. Product pages should link to related products. Collection pages should link to sub-collections and related categories. This web of internal links helps Google understand the topical relationships across your store.

Shopify-Specific SEO Issues

Shopify introduces several platform-specific SEO challenges that you will not encounter on other ecommerce platforms. Understanding and auditing these Shopify-specific issues is essential for a complete SEO review.

Liquid template issues

Shopify's Liquid templating language controls how your store's HTML is generated. Template-level issues affect every page that uses that template, so a single error can impact hundreds or thousands of pages simultaneously. Audit your Liquid templates for:

• Heading hierarchy in templates — Open your product template (product.liquid or main-product.liquid in OS 2.0 themes) and verify the H1 tag wraps the product title. Check that section headings like "You may also like" or "Customer reviews" use H2 or H3 tags, not additional H1 tags.
• Canonical tag implementation — Shopify automatically adds canonical tags in the theme.liquid layout file. Verify that the canonical tag outputs the correct canonical URL. Some custom themes or apps override the default canonical tag behavior and can introduce errors.
• Structured data in templates — Check whether your theme includes Product schema markup in the product template. Verify it includes all required fields: name, description, image, price, priceCurrency, availability, and brand. Test a product page with Google's Rich Results Test to catch any schema errors.
• Meta tag templates — Review how your theme generates meta titles and descriptions. Some themes hardcode a format that appends unnecessary text or truncates titles. Ensure the meta title uses the custom SEO title when available and falls back to the product or collection title when it is not.

Theme code bloat

Shopify themes, especially premium themes with extensive customization options, often include JavaScript and CSS for features you are not using. This bloat directly impacts page speed. Audit your theme by:

• Identifying unused JavaScript — Use Chrome DevTools Coverage panel to see what percentage of your theme's JavaScript actually executes on each page. If large portions are unused, they are adding weight without value.
• Checking for render-blocking resources — View the network waterfall in DevTools and identify CSS and JavaScript files that block rendering. Theme assets loaded in the document head without async or defer attributes delay page rendering.
• Evaluating theme sections — OS 2.0 themes load sections and their associated assets. If you have disabled sections in your theme customizer, check whether their assets still load. Some themes load section assets regardless of whether the section is active.

App impact assessment

Each Shopify app you install can inject scripts and stylesheets into your storefront. Over time, this accumulation of third-party code becomes the primary performance bottleneck. Conduct an app audit by:

• Listing every installed app — Go to your Shopify admin and document every installed app, even ones you think are inactive.
• Testing page speed impact — Disable non-essential apps one at a time and measure the page speed impact of each. This is tedious but reveals which apps are the biggest performance offenders.
• Checking for leftover code — When you uninstall a Shopify app, it does not always remove the code it injected into your theme. Inspect your theme.liquid file and snippet files for script and stylesheet tags referencing apps you have already uninstalled.
• Evaluating necessity — For each app, ask: Does this app generate revenue or improve user experience enough to justify its performance cost? Can its functionality be replicated with native Shopify features or lightweight custom code? Many stores can safely remove 3 to 5 apps without losing any important functionality.

Shopify URL structure limitations

Shopify enforces a fixed URL structure that creates unique audit considerations. Products always live at /products/handle, collections at /collections/handle, and blog posts at /blogs/blog-name/handle. You cannot change these prefixes. During your audit, check for:

• Duplicate product URLs — Products accessible through collection paths (/collections/collection-name/products/product-name) create additional URLs for the same product. Shopify handles this with canonical tags, but verify the canonicals are correct and functioning.
• URL handle optimization — Review product and collection URL handles for keyword relevance. Handles like "product-1234" or auto-generated handles with unnecessary words waste URL real estate. Optimize handles to include primary keywords in a concise format.
• Missing redirects after handle changes — Shopify does not automatically create redirects when you change a URL handle. If you find products or collections with recently changed handles, verify that 301 redirects exist from the old URLs to the new ones.

Essential Audit Tools

The right tools make the difference between a superficial review and a comprehensive audit that catches every issue. Here is the toolkit you need, organized by function and budget level.

Free tools

• Google Search Console — Your most important free tool. Provides indexation data, crawl stats, keyword ranking data, Core Web Vitals field data, and mobile usability reports. Every Shopify store should have Search Console configured and monitored regularly.
• Google PageSpeed Insights — Tests individual page performance and provides both lab data (Lighthouse) and real-user field data (CrUX). Test your homepage, a product page, a collection page, and a blog post to benchmark all your key templates.
• Screaming Frog (free tier) — Crawls up to 500 URLs for free. Sufficient for small to medium Shopify stores. Identifies broken links, missing meta tags, duplicate content, heading structure issues, and more. The paid version removes the URL limit and adds advanced features.
• Google Rich Results Test — Validates your structured data markup. Test product pages, blog posts with FAQ schema, and your homepage to ensure rich results eligibility.
• Chrome DevTools — Built into Chrome. Use the Network tab for waterfall analysis, the Lighthouse tab for performance auditing, the Coverage panel for identifying unused CSS and JavaScript, and the Elements panel for inspecting HTML structure.

Paid tools

• Ahrefs — Comprehensive SEO platform for backlink analysis, keyword research, competitor analysis, content gap identification, and site auditing. The Site Audit feature crawls your entire store and categorizes issues by severity. Essential for the link profile analysis portion of your audit.
• Semrush — Similar to Ahrefs with additional features for keyword cannibalization detection, position tracking, and on-page SEO scoring. The Site Audit tool provides automated issue detection with clear fix recommendations.
• Screaming Frog (paid) — Removes the 500 URL crawl limit and adds JavaScript rendering, custom extraction, page speed integration, and structured data validation. Worth the investment for stores with more than 500 pages.
• ContentKing or Lumar — Real-time SEO monitoring tools that continuously crawl your site and alert you to issues as they appear. Particularly valuable for stores that make frequent changes and want to catch SEO regressions before they impact traffic.

Shopify-specific tools

• Shopify's built-in speed report — Found under Online Store > Themes. Compares your speed against similar stores and highlights specific issues. Less detailed than Lighthouse but useful for a quick benchmark.
• Theme Inspector for Shopify — A Chrome extension from Shopify that shows which Liquid templates and snippets contribute to page load time. Essential for diagnosing theme-level performance issues.

Creating Your Action Plan from Audit Findings

An audit without an action plan is just a list of problems. The real value comes from prioritizing your findings by impact and effort, then executing fixes in a logical sequence that maximizes results in the shortest time.

Prioritization framework

Categorize every finding into one of four priority tiers:

• Critical (fix immediately) — Issues that actively prevent Google from indexing your content or that are causing significant traffic or revenue loss. Examples: robots.txt blocking important pages, canonical tags pointing to 404 pages, entire sections of your store not indexed, site returning 500 errors.
• High priority (fix within 2 weeks) — Issues that meaningfully impact rankings or user experience for a large number of pages. Examples: missing title tags on product pages, Core Web Vitals failures on key templates, redirect chains on high-traffic pages, missing structured data.
• Medium priority (fix within 1 month) — Issues that affect individual pages or have a moderate impact on overall SEO performance. Examples: thin product descriptions, missing alt text, suboptimal internal linking, meta descriptions that need rewriting.
• Low priority (fix within quarter) — Nice-to-have improvements that provide incremental gains. Examples: optimizing URL handles for better keyword targeting, adding content to collection pages that already rank well, cleaning up minor redirect chains.

Execution sequence

Follow this sequence to maximize the impact of your audit fixes:

1. Fix critical technical blockers first — Resolve any issues that prevent Google from crawling and indexing your store properly. No other optimization matters if Google cannot see your pages.
2. Address template-level issues — Fixes to Liquid templates, theme code, and structural elements affect every page that uses that template. A single template fix can improve hundreds or thousands of pages simultaneously.
3. Optimize high-traffic pages — Focus your on-page and content improvements on pages that already receive traffic or rank in positions 4 through 20. These pages are close to generating meaningful traffic and are most responsive to optimization.
4. Fill content gaps — Create new content targeting keywords your competitors rank for but you do not. Prioritize keywords with high commercial intent and reasonable competition.
5. Build ongoing monitoring — Set up weekly monitoring of Google Search Console for new crawl errors, indexation changes, and Core Web Vitals regressions. Schedule quarterly re-audits to catch new issues before they accumulate.

Measuring audit impact

Track these metrics before and after implementing your audit fixes to quantify the impact:

• Indexed pages — Count of pages indexed in Google Search Console. Should increase as you fix indexation issues.
• Organic traffic — Total organic sessions and revenue. Allow 4 to 8 weeks after implementing changes before expecting measurable improvements.
• Core Web Vitals pass rate — Percentage of URLs passing all three Core Web Vitals thresholds. Monitor in Search Console's Core Web Vitals report.
• Average position — Track average ranking position for your target keywords. Focus on movement in the top 20 where ranking improvements translate to traffic.
• Crawl efficiency — Ratio of crawled pages that return 200 status codes. Should improve as you fix broken links and redirect issues.

Conclusion

A Shopify SEO audit is not a one-time project—it is the starting point of an ongoing optimization process. The audit reveals where you stand today, the action plan defines where you need to go, and consistent execution and monitoring ensure you get there.

Start with the technical foundation. Fix crawl errors, resolve indexation issues, and ensure your theme is not sabotaging your performance. Then move to on-page elements: optimize every title tag, meta description, heading, and image across your store. Audit your content for thin descriptions, duplicate text, and keyword cannibalization. Analyze your link profile for toxic links and internal linking gaps. And address the Shopify-specific issues—Liquid template errors, app bloat, and URL structure limitations—that other audit guides overlook.

The stores that dominate organic search are not the ones with the biggest budgets or the most products. They are the ones that systematically identify and fix every issue standing between their store and the top of Google's results. This audit guide gives you the framework to do exactly that.