Shopify Technical SEO Audit: Fix Crawl Errors and Indexation Issues Using Google Search Console

TL;DR

If your Shopify store isn't gaining organic traffic despite publishing new pages, Google likely can't see them. This guide shows you exactly how to use Google Search Console's Coverage report to find 404 errors, duplicate canonicals, thin-content exclusions, and crawl budget problems - and fix them step by step.

Why Technical SEO Has to Come First

Before you write a single line of collection page copy or chase a backlink, your Shopify store needs a clean technical foundation. Here's why: indexation is binary. Either Google can crawl and index your pages, or it can't. All other SEO work is wasted if you're building on broken infrastructure.

Across 70+ Shopify store audits, fixing crawl errors and indexation issues alone improved indexed page counts by 30 - 50% within two to four weeks - before any new content was published.

The sequence is: fix technical first, then optimize.

Step 1: Open the Coverage Report in Google Search Console

Go to Google Search Console, select your property, and navigate to Indexing > Pages (older accounts show this as Coverage).

You'll see four buckets:

Your audit works through each of these in order, starting with Errors.

Step 2: Resolve Crawl Errors

404 Errors (Page Not Found)

These are the most common errors on Shopify stores. They appear when a product is deleted, a collection is renamed, or a URL changes without a redirect being set.

Why it matters beyond just broken pages: Crawl budget is finite. Every 404 Googlebot hits is a wasted request that could have gone to a live, rankable product or collection page.

Fix it:

1. Click the 404 category in the Coverage report and export the affected URLs.
2. For each URL, decide: was the content removed permanently, or did the URL change?
3. If the URL changed: set a 301 redirect from the old URL to the new one.
4. In Shopify, manage this at Online Store > Navigation > URL Redirects.
5. If the content is genuinely gone but the URL had inbound links, redirect to the closest relevant live page.

Server Errors (5xx)

Less frequent but more urgent. A 5xx means your server failed to respond to Googlebot. A cluster of these can signal a conflicting app, a theme issue, or a hosting problem. Left unresolved, it trains Google to crawl your store less frequently.

Fix it: Identify whether the errors are isolated or widespread. Check recently installed apps and theme changes. If widespread, contact your hosting or a developer immediately.

Step 3: Investigate the Excluded Tab

This is where the less obvious - and often more impactful - problems live.

"Duplicate, Google chose different canonical than user"

This is specific to how Shopify's URL architecture works. When a product appears in multiple collections, Shopify generates multiple URLs:

• /collections/skincare/products/vitamin-c-serum
• /collections/bestsellers/products/vitamin-c-serum

Shopify is supposed to handle this by pointing both to the canonical at /products/vitamin-c-serum. But third-party apps and theme modifications frequently break this.

Fix it:

1. Open an affected product page in your browser.
2. Right-click > View Page Source, then search for canonical.
3. Confirm it points to /products/[handle] - not a collection-scoped URL.
4. If it's wrong, trace the issue to your theme's liquid files or a conflicting SEO app and correct it.

"Crawled - currently not indexed"

Google reached the page but decided it wasn't worth indexing. On Shopify stores, this almost always means:

• Thin content: Collection pages with no descriptive text, or product pages with minimal copy.
• Duplicate descriptions: Multiple products sharing auto-generated boilerplate copy.

Fix it: For collection pages you want to rank, add 150 - 300 words of unique introductory copy above the product grid. For products, ensure descriptions are specific and non-duplicate.

"Excluded by 'noindex' tag"

The page is explicitly telling Google not to index it. This is correct for checkout, cart, and account pages - but occasionally surfaces collection or product pages due to a theme update or app misconfiguration.

Fix it: View the source of any flagged page you want indexed and search for noindex. If present, track it down in your theme liquid files or SEO app settings and remove it.

"Blocked by robots.txt"

Check yourdomain.com/robots.txt directly. Shopify correctly blocks /cart and /checkout by default. If collection or product pages are appearing here, something has gone wrong. Edit carefully - an incorrect robots.txt can deindex your entire store.

Step 4: Check Crawl Stats for Structural Problems

In Search Console, go to Settings > Crawl Stats. Look at how many pages Googlebot crawls daily versus how many pages are actually indexed.

A large gap usually means Googlebot is burning crawl budget on parameter-generated URLs like:

• /collections/mens-sweaters?color=blue&size=medium
• /collections/tees?sort_by=price-ascending

These can multiply your apparent page count by thousands while adding zero indexable value.

Fix it: Ensure canonical tags on filtered and sorted collection URLs point back to the base collection URL. This consolidates crawl signals and stops Googlebot from wasting time on variants.

The Audit Checklist (Repeatable Sequence)

1. Open Coverage report → record totals for Error, Valid, Excluded.
2. Export all 404 errors → set up 301 redirects in Shopify for any that had traffic or inbound links.
3. Review Excluded tab → prioritize "Duplicate canonical" and "Crawled - not indexed."
4. Spot-check important collection and product pages for accidental noindex tags.
5. Check Crawl Stats → flag any large gap between crawl requests and indexed pages.
6. Return in 2 - 4 weeks → compare Coverage totals to confirm improvements.

What Comes Next

A clean technical foundation is what makes everything else - collection page copy, internal linking, backlinks - actually register in Google's index. None of it compounds if Google is spending crawl budget on 404 pages or silently excluding your collection pages as duplicates.

Start with the Coverage report. Fix what's broken. Then build.

If you want a team that runs this process on Shopify stores every day, New Seas handles technical SEO audits and ongoing ecommerce SEO for Shopify brands. Visit newseas.co to learn more.