Ecommerce SEO Audit: 30-Point Checklist for Online Stores

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Most ecommerce SEO audits are either too shallow to be useful (a Lighthouse score and a list of broken links) or too deep to be actionable (a 200-page PDF nobody reads). A good audit sits between those: comprehensive enough to surface every issue that matters, focused enough that a non-technical owner can prioritise the fixes.

After a decade of running ecommerce SEO audits, the issues that turn up most often are the same eight or nine, and the highest-impact fixes are rarely the ones audit reports lead with. This guide is the 30-point framework I work through on every new ecom client. It’s the same process we use for free first-pass audits.

This guide is a complete checklist for auditing a Shopify or other ecommerce store. It covers technical SEO, on-page optimisation, collection and product pages, schema, internal linking, the Merchant Center feed, speed and Core Web Vitals, and mobile. Work through it sequentially or skip to the section relevant to your current problem. It is the closing piece of our ecommerce SEO cluster: Shopify SEO guide, collection page SEO, product page SEO, ecommerce keyword research, and product feed optimisation.

How to Use This Audit

Score each item with a status: Pass, Needs attention, or Fail. Pair each Needs attention or Fail with a specific fix and an estimated impact level. Work top-down through the priority order at the end, not section-by-section. A failed canonical on variants is worth fixing before a missing alt tag on a marketing image.

Time required: a thorough first-pass audit on a store with 100-500 products takes 4-6 hours. Catalogues over 5,000 SKUs usually need 8-12 hours plus tool licenses (Screaming Frog Pro, Ahrefs, etc.).

Section 1: Technical SEO Audit

The foundation. If the technical layer is broken, nothing else compounds.

• 1. XML sitemap submitted and indexed. Check /sitemap.xml resolves, contains current product and collection URLs, and is submitted in Google Search Console. Confirm Indexing report shows reasonable submitted-vs-indexed ratio (target 90%+).
• 2. Robots.txt configured correctly. On Shopify, edit via robots.txt.liquid. Confirm /cart, /checkout and admin paths are blocked. Confirm no critical URLs are accidentally blocked.
• 3. Canonical tags correct on all page types. View source on a product, collection, blog post, and variant URL. Each should have a self-referential canonical or (in the variant case) point back to the base product URL.
• 4. No “noindex” tags on pages that should be indexable. Crawl with Screaming Frog and filter for noindex tags. Cross-check against pages you want ranking.
• 5. HTTPS enforced and HTTP redirects to HTTPS. Test by visiting http:// versions of key URLs. Confirm 301 redirect to HTTPS.
• 6. No mixed content warnings. Check browser console on home, product, collection pages. Mixed content from third-party widgets is the most common cause.

Section 2: On-Page SEO Audit

• 7. Custom meta titles set on all important pages. Spot-check 10 collections, 20 products, the home page, and the about/contact pages. Default-generated titles signal a missed optimisation opportunity.
• 8. Meta descriptions set and within length (150-160 characters). Same spot-check. Missing meta descriptions get auto-generated by Google, usually poorly.
• 9. H1 hierarchy correct on every page type. Audit home page, product, collection, blog templates. Confirm one H1 per page, matching the page topic. Watch out for theme-injected H1s in carousel or featured sections.
• 10. Image alt text on top-selling products. Export from Shopify or audit with Screaming Frog’s images report. Missing alt text on key product images hurts both accessibility and image search.

Section 3: Collection Page Audit

• 11. Custom intro copy above the product grid. Audit your top 15 collections. Default theme behaviour shows only the title and grid. Custom intro copy is the highest-impact change you can make to a collection page.
• 12. Long-form content below the grid. 400-800 words covering category context, buying considerations, and related semantic terms. Most stores skip this and lose meaningfully to competitors who don’t.
• 13. FAQ section with FAQPage schema. 5-8 real questions per major collection.
• 14. Filter URLs handled (noindex/nofollow where appropriate). Run Screaming Frog with parameter URL exploration enabled. Surface every filter URL pattern and decide which should be indexable.
• 15. Strategic collections in main navigation. Your top revenue-generating collections deserve top-level navigation slots. Hidden behind filters or in mega-menu sub-sub-items is wasted link equity.

Section 4: Product Page Audit

• 16. Unique custom descriptions on top-selling products. Export descriptions and sample 20. Manufacturer copy or repeated boilerplate signals a major gap.
• 17. Multiple high-quality images per product. Aim for 5-10 images on higher-consideration items, 3-5 on commodity. Each image with descriptive alt text and reasonable file size.
• 18. Specifications block in scannable format. Materials, dimensions, weight, care, country of origin. Both for customers and for structured data extraction.
• 19. Reviews displayed (where compliant). Non-AHPRA categories should show reviews and emit Review/AggregateRating schema. AHPRA-regulated industries (medical, dental, allied health, cosmetic clinics) cannot.
• 20. Variant canonicals point back to base product URL. View source on a variant URL. Common breakage point on older themes.

Section 5: Schema Markup Audit

• 21. Product schema validates on every product page template. Run Google’s Rich Results Test on 3-5 representative product pages. Confirm Product schema with at least: name, image, description, brand, sku, offers (price/currency/availability), aggregateRating (where applicable).
• 22. Organization schema on the home page. Includes name, url, logo, sameAs links to social profiles. Foundation for AI search citation.
• 23. BreadcrumbList schema on product and collection pages. Often emitted by themes automatically but worth verifying.

For deeper schema setup, see our schema markup implementation guide.

Section 6: Internal Linking Audit

• 24. Strong inbound links to top revenue collections. Run a Screaming Frog crawl and check inbound link counts. Top collections should have 50+ internal inbound links across the site.
• 25. Blog content linking to relevant collections and products. Audit your top 10 blog posts. Each should have 2-5 contextual links to commercial pages where natural. Most blog posts are written in isolation and miss this.
• 26. Related product blocks on product pages. Auto-generated by most themes, but check the logic. Random “you may also like” widgets are weaker than curated cross-sells based on actual category or use case.

Section 7: Merchant Center Feed Audit

• 27. Feed approved and active in Merchant Center. Check the Products section for disapprovals, warnings, and pending items.
• 28. Required attributes complete: title, description, price, availability, link, image_link, brand, gtin. Missing required attributes auto-disapprove products. Optional but recommended: mpn, google_product_category, item_group_id (for variants), shipping, color, size, material.
• 29. Feed prices match website prices to the cent. Mismatches trigger price disapprovals and pull products from Shopping ads entirely.

The full feed playbook is in our product feed optimisation guide.

Section 8: Speed and Core Web Vitals Audit

• 30. PageSpeed Insights mobile score above 50 on key page templates. Test home, top collection, top product. Below 50 usually means heavy theme or excessive app scripts. Above 70 is the target. Below 30 needs immediate attention.

Practical speed wins on Shopify, in order of impact:

• Remove apps you are not actively using. Each app adds at least one script.
• Migrate to a modern theme (Online Store 2.0 architecture) if you’re on a pre-2021 theme.
• Compress source images. Shopify will serve WebP but heavy source files still hurt LCP.
• Defer non-critical third-party scripts (chatbots, popups, social widgets).
• Lazy-load below-the-fold images. Most modern themes do this; older themes don’t.

The 30-Point Priority Order

If you only fix the top 10 from any audit, focus on these. They produce the largest gains for most ecommerce stores:

1. Custom long-form content on top 10 collection pages
2. Unique custom descriptions on top 20 product pages
3. Product schema completeness on every product page template
4. Filter URL crawl waste audit and noindex strategy
5. Variant canonical correctness
6. Image alt text and file naming on top-selling products
7. Strategic collections placed in main navigation
8. Merchant Center feed audit and fix list
9. Speed audit and app cleanup
10. Internal links from blog content to commercial pages

Tools I Actually Use for Ecommerce SEO Audits

• Screaming Frog SEO Spider for crawling, parameter URL discovery, response codes, canonical and meta tag auditing. The single most useful technical SEO tool.
• Google Search Console for indexing status, query performance, Core Web Vitals data, and manual action checking.
• Google PageSpeed Insights for Core Web Vitals on individual page templates.
• Google Rich Results Test for validating schema markup.
• Google Merchant Center Diagnostics tab for feed quality and product-level disapprovals.
• SE Ranking for keyword tracking, competitor analysis, and rank movement over time.
• Shopify admin reports for sales, conversion, and inventory data that informs prioritisation.

Section 9: Backlink and Off-Page Audit

Backlinks are the part of the audit most ecommerce owners skip. I run this section last because the on-site issues need to be fixed before any new links pointing at broken or thin pages are wasted.

Pull the referring domains report from Ahrefs, Semrush or SE Ranking and sort by Domain Rating. I’m looking for three things: the total referring domains compared to the top three competitors, the ratio of branded versus non-branded anchor text, and the spread of links across product, collection and blog URLs. Most Shopify stores I audit have 80 to 90 percent of their links pointing at the homepage, which is wasted equity. The Black Finch Jewellery case study at /results/ shows how rebalancing internal anchors and adding 12 deep links to collection pages moved the engagement ring category from page three to position four in nine weeks.

Then run a toxic link check. Disavowing is almost always unnecessary in 2026, but I look for paid link footprints from previous agencies, especially expired domain redirects pointing at the store.

Finally, do a backlink gap. Export the referring domains for your top three competitors and filter for sites that link to two or more of them but not to you. That filtered list is your outreach shortlist for the next quarter.

Section 10: Faceted Navigation and Crawl Budget Audit

Faceted navigation is the single biggest crawl budget sink on a Shopify or WooCommerce store. Every filter combination (colour, size, price, brand) generates a parameterised URL, and by default Google will crawl and try to index every permutation. On a 2,000-product store that can balloon to 400,000 crawlable URLs.

Open Search Console and check the Pages report for the count under “Crawled, currently not indexed” and “Discovered, currently not indexed.” If either number is more than three times your actual product count, faceted URLs are eating your crawl budget. Then run a Screaming Frog crawl with parameter handling off and look at the URL count by parameter. On Fanzy Pantz the initial crawl returned 38,000 URLs against a catalogue of 600 products. Almost all of them were colour and size filter combinations.

The fix is a tiered approach. First, decide which filtered URLs deserve to rank. Single-attribute filters with real search demand (for example “black bridesmaid dresses”) get their own optimised collection page with a unique handle. Multi-attribute combinations get noindex via robots meta. Internal links pointing at faceted URLs get nofollow, and the URLs themselves get blocked in robots.txt only after the noindex tags are picked up.

Verify in Search Console four weeks later. The Crawl Stats report should show fewer requests to parameter URLs and more to product and collection pages. That redirected crawl budget is what lifts new product launches into the index faster.

Section 11: Competitor and Keyword Gap Audit

The audit isn’t complete until you know what you’re not ranking for that you should be. I treat this as a structured section because the output feeds directly into the content plan that comes after the audit.

Start by identifying three direct competitors. Direct means they sell the same product category to the same market, not the biggest names in the vertical. For Black Finch Jewellery the direct competitors are independent Australian fine jewellers in a similar price bracket, not Tiffany or Michael Hill. Pull each competitor’s top 1,000 ranking keywords from SE Ranking or Ahrefs.

Run a keyword gap report filtered to keywords where at least two of the three competitors rank in the top 20 and your store doesn’t rank at all. Sort by search volume and filter out branded terms. What’s left is your gap list. On Apero Label this exercise surfaced 47 maternity-specific informational keywords (sizing guides, fabric care, trimester-by-trimester wear) that all three competitors had blog coverage for and Apero had none.

Then do a collection gap. Look at the URL structures of competitor collection pages. If two of three competitors have a /collections/linen-dresses page and you don’t, that’s a missing collection. Add it to the audit output as a “new page required” task, separate from the optimisation tasks for existing pages.

This section turns the audit from a defensive document (fix what’s broken) into an offensive one (here’s where the next 12 months of growth comes from).

Section 12: AI Search and AI Crawler Audit

AI-driven traffic is now showing up in GA4 as a distinct referrer set (ChatGPT, Perplexity, Gemini, Claude) and the optimisation work is different from traditional SEO.

Start with crawler access. Open robots.txt and check that GPTBot, Google-Extended, PerplexityBot, ClaudeBot and OAI-SearchBot are not disallowed. Many Shopify stores inherited a blanket AI block from a 2024 theme update or a privacy plugin. If you want product pages cited in AI answers, those crawlers need read access. On Fanzy Pantz the default Shopify robots.txt was fine, but a Shopify privacy app had injected a Disallow for GPTBot that took 20 minutes to find.

Next, check your citation footprint. Run your top 20 commercial queries through ChatGPT, Perplexity and Google AI Overviews. Note which sources get cited. If competitor PDPs or blog posts are cited and yours aren’t, the gap is almost always content depth and FAQ formatting. AI engines preferentially cite pages with clear question-and-answer structure, specific numbers (sizing, materials, dimensions), and original photography.

Finally, add FAQ blocks with FAQPage schema to your top 10 collection pages and top 20 product pages. On Black Finch Jewellery, adding a 6-question FAQ to each engagement ring collection page produced citations in Perplexity for “how to choose an engagement ring Australia” within six weeks. The traffic from those citations is small but the assisted conversions are not.

Section 13: Australian Compliance and Local Trust Signals Audit

For any store selling to AU customers, this is a quiet revenue leak.

The audit checks five things. First, ABN visibility. The ABN should appear in the footer, on the About page and inside the Organization schema as a sameAs reference to the abr.business.gov.au lookup. Google treats verified business registration as a trust signal, and AU shoppers actively look for it before buying from independent stores.

Second, shipping and returns clarity for AU shoppers. The shipping policy needs to specify AU delivery times by state, the returns window in business days (AU consumer law is stricter than US norms), and any GST inclusivity statement on prices.

Third, currency and price schema. AUD should be set as the default currency in product schema, not just in the storefront. I’ve seen Shopify stores where the schema price was in USD because of a theme misconfiguration, which causes Google Shopping to disapprove the product.

Fourth, AU-specific structured data. LocalBusiness schema for any brick-and-mortar storefront, Service Area schema if you ship nationally, and Organization schema with the registered Australian address.

Fifth, AU spelling consistency. Optimise, colour, jewellery, organise. Google AU treats spelling variants as ranking signals for AU-targeted queries. On Black Finch Jewellery, standardising “jewellery” across 180 product pages (it had been mixed jewellery/jewelry from a US theme) lifted impressions on jewellery-spelled queries by 34 percent in two months.

Section 14: Agentic Shopping Readiness Audit

Agentic shopping is the layer where AI assistants (ChatGPT shopping, Perplexity, Google’s Gemini-powered Search) don’t just cite product pages, they complete the purchase comparison on the user’s behalf. For that to work, the agent needs structured, machine-readable answers to four questions on every product page: what is it, what does it cost in the user’s currency, is it in stock, and how does it ship.

The audit checks four things. First, Product schema completeness. Every product needs price, priceCurrency, availability, sku, gtin (where available), and shippingDetails. Shopify outputs most of this by default but theme customisations frequently strip shippingDetails. Validate every product type in Google’s Rich Results Test.

Second, MerchantReturnPolicy schema. Required for agentic shopping engines to compare return terms. Most Shopify stores I audit have this missing entirely.

Third, structured shipping data in the Merchant Center feed (shipping_weight, shipping_label, ships_from_country). Agentic engines pull from MC feeds where available.

Fourth, an /llms.txt file at the root. This is a plain text file listing your most important product and collection URLs with one-line descriptions. Adoption is early but growing, and the cost of adding one is roughly 15 minutes per store. On Apero Label I added an llms.txt covering 40 priority URLs in May and the file has been fetched by GPTBot, ClaudeBot and PerplexityBot weekly since.

Want a Free Ecommerce SEO Audit?

If you run a Shopify or other ecommerce store and want a fresh set of eyes on your store, we offer a free first-pass audit using the 30-point framework above. We send back a written report with priority fixes ordered by likely impact. No commitment, no obligation.

Request your free ecommerce SEO audit →

Frequently Asked Questions

What is an ecommerce SEO audit?

An ecommerce SEO audit is a structured review of an online store’s organic search performance across technical SEO, on-page optimisation, collection and product pages, structured data, internal linking, the Merchant Center feed, speed, and mobile experience. The output is a prioritised list of fixes ordered by likely impact, not just a list of issues.

How long does an ecommerce SEO audit take?

A thorough first-pass audit on a store with 100-500 products takes 4-6 hours. Catalogues over 5,000 SKUs usually need 8-12 hours plus paid tool licenses (Screaming Frog Pro, Ahrefs, etc.). Quick top-line audits can be done in 60-90 minutes but miss most of the depth.

What tools do I need to audit my Shopify store?

Free tools: Google Search Console, PageSpeed Insights, Rich Results Test, Merchant Center Diagnostics. Paid tools that make the audit faster: Screaming Frog SEO Spider, SE Ranking or Ahrefs for keyword and competitor data. For most stores, free tools plus Screaming Frog (paid) cover 80% of the workflow.

How often should I audit my ecommerce store for SEO?

A full audit annually, with a quarterly review of Search Console data, Core Web Vitals, and Merchant Center diagnostics. After any major site change (theme migration, replatform, large catalogue update), trigger a fresh audit immediately to catch regressions.

What are the most common ecommerce SEO issues?

Collection pages with no content beyond the product grid. Manufacturer-default product descriptions copied verbatim. Filter URL crawl waste from faceted navigation. Incomplete Product schema (missing gtin, mpn, aggregateRating). Variant canonicals broken on older themes. Heavy theme and app stack hurting Core Web Vitals. These six account for 80% of the issues I find on first audits.

Should I fix everything on an SEO audit or prioritise?

Prioritise. A 30-point audit usually surfaces 15-20 things that need attention. Trying to fix all of them simultaneously means none get done well. The priority order at the end of this guide is a sensible starting point for most stores.

What is the biggest leverage point in ecommerce SEO?

Collection page architecture and content. Most stores have collections with title + product grid and nothing else. Adding intro copy, long-form content, FAQ sections, and proper internal linking to the top 10-15 collections is the highest-impact SEO investment for most Shopify stores. Our collection page SEO guide covers the implementation in detail.

How do I know if my ecommerce SEO is working?

Key indicators: organic clicks growing month over month in Search Console, non-brand impression share rising, keyword positions improving for tracked terms in SE Ranking, conversion rate stable or improving on organic traffic specifically. Revenue impact lags clicks by 4-8 weeks for most stores. Avoid optimising for traffic in isolation; pair every SEO improvement with conversion and revenue measurement.