Every product you sell has two URLs.
Shopify creates /products/handle and /collections/x/products/handle for the same item, then sets the canonical to the first. But most themes link internally to the second, so your canonical tags say one thing and every internal link on the site says another. On every product in your catalogue. It takes ten seconds to check.
Six things a general SEO agency won't find.
These exist because you're on Shopify. They don't appear in a standard site audit, because a standard audit doesn't know the platform generates them by default.
Check this yourself, right now
Your links say: /collections/footwear/products/blue-running-shoe
Open any product from a collection page and look at the address bar. Then view source and find the canonical tag. If they disagree, that's the default Shopify behaviour, and it's on every product you sell.
Shopify handles the canonical correctly. What it doesn't do is make your theme's internal links match. So every link on your site points at a URL you've told Google to ignore, which wastes crawl budget and dilutes the signal you're trying to send.
Two stores built with the structure right from the start.
These Shopify builds show what happens when SEO fundamentals are considered during development, not after problems appear. From collection architecture and canonical URLs to product and variant data, the underlying structure was designed to keep the stores crawlable, organized, and free from unnecessary URL conflicts.
A seasonal, single-category D2C brand launched from scratch on Shopify. No legacy theme to inherit problems from, so collection structure and canonical URLs were set up correctly from day one instead of retrofitted after the fact.
What we did: built the theme and collection hierarchy with internal links matching canonical URLs from launch, the structural work most existing Shopify stores only get around to after something breaks.
A premium catalogue with size and tin variants, exactly the kind of product structure that tends to spawn duplicate, competing URLs once bundling and upsell logic get layered in.
What we did: structured product variants and bundles so the catalogue expansion didn't split into pages competing against each other for the same search terms.
Three services, no overlap.
Shopify stores usually need two of these three, and it's rarely obvious which. Here's the honest split so you don't buy the wrong one.
- Canonical and internal link conflicts
- Faceted navigation control
- Leftover app code removal
- Variant URL handling
- Product Group schema
- Collection page structure
- Keyword and intent research
- Content production and briefs
- Category page targeting
- Link building and digital PR
- Competitor gap analysis
- Works on any platform
- Custom theme development
- App stack audit and cleanup
- Product and collection templates
- Checkout configuration
- Platform migration
- Redirect mapping at launch
Three phases. Most of the value lands in the first month.
Because these are structural fixes rather than a content programme, the work front-loads.
Crawl it properly
Full crawl against the canonicals, indexation checked in Search Console, theme inspected for leftover app code, and filter URLs counted. You get the findings whether you continue or not.
Weeks 1–2Edit the theme
Internal link output corrected, faceted navigation controlled, dead app code stripped, schema extended for variants. Changes made on a duplicate theme and tested before publishing, never edited live.
Weeks 2–5Confirm it took
Crawl stats and indexation monitored to confirm the fixes registered. Shopify updates themes and apps get installed, so this needs revisiting, which is where ongoing work earns its place, if you want it.
OngoingThis is a project, not a retainer.
Most of this work finishes. You fix the structural problems once, and they stay fixed until something changes. We'd rather say that than sell you a monthly fee for a job with an end.
Technical audit
$2,500 one-time · 2 weeks
Start here if: you want to know what's actually wrong before committing, or you'd rather hand the list to your own developer.
- Full crawl checked against canonicals
- Indexation reviewed in Search Console
- Theme inspected for leftover app code
- Filter and variant URLs counted
- Fix list, specific enough to hand over
Audit and fix
$6,500 one-time · 4–5 weeks
For: stores that want it done rather than documented. Theme edits made, tested and published.
- Everything in the audit
- Internal link output corrected in Liquid
- Faceted navigation brought under control
- Dead app code stripped from the theme
- Product Group schema for variants
- Tested on a duplicate theme, then published
Ongoing SEO
From $5,000 per month
Only if you want the wider programme: keyword research, content, category targeting, link building. That's eCommerce SEO, not this page.
- Keyword and intent research
- Content production and briefs
- Collection page targeting
- Link building and digital PR
- Technical health monitored alongside
- Audit fee credits against the fix. If you take the list to your own developer instead, that's a perfectly good outcome and the list is written to be handed over.
- We work on a duplicate theme. Nothing is edited live, everything is tested before publishing, and you keep the backup.
- Rebuilding the store anyway? This work is included in a Shopify build, don't buy it twice.
Before you call.
Is Shopify actually bad for SEO?
No. Shopify handles many SEO fundamentals well, including clean markup, automatic XML sitemaps, HTTPS, and canonical tags. The bigger issue is how Shopify's URL structure, themes, apps, filters, and product variants can create technical SEO problems.
For example, Shopify can expose products through both /products/handle and /collections/x/products/handle. If internal links consistently point to the collection-based URL while the canonical points to the product URL, the site can send mixed signals to search engines. Faceted navigation, duplicate variant URLs, and leftover app code can add further crawl and indexation issues.
How is this different from your eCommerce SEO service?
Clean split. This page is problems Shopify creates. Canonical conflicts, faceted navigation, variant URLs, theme-level schema: things that wouldn't exist on another platform.
eCommerce SEO is the wider discipline: keyword research, content production, category targeting, link building. Platform-agnostic, and it's a monthly programme rather than a project.
Most Shopify stores need both, and the technical work should come first, there's no point ranking content on a site that's splitting its own authority.
Can an SEO app fix this instead?
Not the important parts. Apps sit on top of the theme; these problems live inside it. An app can flag a missing meta description. It can't rewrite how your product links are generated in Liquid, because that's template code.
There's also an irony worth noting: SEO apps add JavaScript to every page load, so installing three of them to fix your technical SEO makes your Core Web Vitals worse. We've audited stores running four SEO apps where every internal link still pointed at the wrong URL.
What does it cost, and is it ongoing?
It's a project, not a retainer. The audit is $2,500. Audit plus implementation is $6,500 over four to five weeks. Then it's done, these are structural fixes that stay fixed.
Ongoing monthly work is optional and it's a different service: content, keywords and links, which is eCommerce SEO. We'd rather tell you the technical job finishes than invoice you monthly for something with an end.
How long before we see results?
Technical SEO changes need to be crawled and processed by search engines before their impact becomes visible. You may see changes in crawling and indexation within four to eight weeks, while ranking improvements can take longer depending on the site's authority, competition, and existing content.
Technical SEO removes structural barriers, but it does not create search demand. Ranking for competitive keywords still requires relevant, high-quality content and authority.
Will you edit our live theme?
No. We duplicate the theme, make changes there, test them, and publish once you've approved. You keep the original as a backup and every change is documented so another developer could follow it.
If you'd rather your own developer implemented our findings, that works too, the audit is written to be handed over rather than to require us.
We're rebuilding the store anyway. Do we need this separately?
No, and don't buy it twice. All of this is included in a Shopify build, because a new theme is where you'd fix link output and schema anyway.
This page exists for stores that are happy with their theme and don't want a rebuild. If a rebuild is on the table, that's the better conversation.
Need more than the technical fix?
Send us the store URL. Nothing else needed.
We'll crawl it publicly and tell you whether your internal links match your canonicals, how many filter URLs are crawlable, what leftover app code is still loading, and whether your variants are competing with each other. No store access required, it's all visible from outside, which is rather the point.
No store access needed · No obligation · Findings are yours to hand to any developer