How Do I Run a Free Shopify SEO Audit with Ahrefs + Claude?

You don't need a $200/mo Ahrefs plan to run a real SEO audit on your Shopify store. The free stack covers what an operator actually needs. Part of our AI workflows pillar. Companion to the main loop walkthrough: how do I use Claude to run SEO for Shopify.

The customer pain point

Two failure modes show up over and over:

"I tried doing SEO myself but every tool wanted $99–$399/mo before showing me anything useful."
"I exported the data but it was 600 rows of warnings and I didn't know what to fix first."

Both solvable. The free stack handles (1). Claude with the right prompt handles (2). This post is the recipe for both.

The Free Stack
Step 1 — Verify Ahrefs Webmaster Tools
Step 2 — Pull GSC Performance
Step 3 — Core Web Vitals on Top Pages
Step 4 — Backlink + Authority Snapshot
Step 5 — Hand Everything to Claude
What the Free Stack Misses

Key Takeaways

Tool	What you get free	What you'd pay for elsewhere
Ahrefs Webmaster Tools	Full site audit, top pages, top backlinks	$99/mo (Lite)
Google Search Console	Real queries, impressions, CTR, indexing	Free always
PageSpeed Insights	Core Web Vitals + Lighthouse per URL	Free always
Ahrefs Backlink Checker	Top 100 backlinks per domain	Bundled in paid plans
Ahrefs Website Authority Checker	Domain Rating	Bundled in paid plans
Ahrefs Keyword Generator	150 keyword ideas + KD	$99/mo (Lite)

Total: $0. Enough for a real audit on one Shopify store.

The Free Stack

The five tools you'll use:

Ahrefs Webmaster Tools (AWT) — the workhorse. Site audit, top pages, top backlinks, search traffic estimates. Free for sites you own.
Google Search Console (GSC) — ground truth for impressions, clicks, queries, indexing. Always free.
PageSpeed Insights — Core Web Vitals (LCP, CLS, INP) per URL. Free.
Ahrefs free widgets — backlink checker, website authority, keyword generator. Free, no signup.
Claude — the brain that ranks the fixes.

Everything below is a 60–90 min, one-time setup. After that the re-audit is ~20 min.

Step 1 — Verify Ahrefs Webmaster Tools

Sign up at ahrefs.com/webmaster-tools → Add a project → enter your Shopify domain (custom domain, not *.myshopify.com).

Verification options:

HTML file upload — put the file in your Shopify theme's assets/ folder, then reference it from a route. Awkward on Shopify because there's no static file root.
DNS TXT record — easier. Add the TXT record in your domain registrar (Cloudflare, Shopify domains, etc.). Takes 5 min + DNS propagation.
Google Analytics or Google Tag Manager — if you already have either installed, this is one click.

Once verified, AWT crawls your site. Wait 24–48 hours for the first full audit.

What to export:

Site Audit → All issues → Export CSV (this is the primary input for Claude)
Top Pages → Top 50 by traffic → Export CSV
Top Backlinks → Export CSV (you'll cross-reference for disavow candidates)

Step 2 — Pull GSC Performance

In Search Console → Performance:

Set date range to last 3 months.
Add filters: Query is not "brand name" (strip branded traffic — it's noise for SEO decisions).
Click Export → CSV (downloads Queries.csv with query + clicks + impressions + CTR + position).

Then check Coverage → Indexing:

Note any "excluded" or "error" URLs, especially anything that matches your top revenue products/collections. These are pages Google can't or won't index.

Then check Core Web Vitals in GSC for the URL-level breakdown.

The two GSC exports + the coverage list are your second input bundle.

Step 3 — Core Web Vitals on Top Pages

GSC gives you site-level CWV. PageSpeed gives you the per-URL detail you need to actually fix anything.

For each of these 7 URLs, run pagespeed.web.dev on mobile (mobile is what Google ranks against):

Homepage
Top 3 collection pages by revenue
Top 3 product pages by revenue

Record for each: LCP (target <2.5s), CLS (target <0.1), INP (target <200ms), and the top 3 opportunities Lighthouse flags.

A quick way to compile this: take screenshots of each report and paste them into the Claude prompt, or copy the "Diagnostics" section as text.

Step 4 — Backlink + Authority Snapshot

Two free Ahrefs widgets, no signup needed:

Backlink Checker — paste your domain → shows top 100 backlinks. Useful for: spotting toxic links (spam directories, PBN footprints) and finding underused brand mentions to chase down.
Website Authority Checker — your Domain Rating (DR). Then run your top 3 competitors through it. If your DR is 12 and competitors are 38, the SERP gap explains itself.

Bonus — Keyword Generator — paste a seed keyword (your top category) → 150 ideas with rough Keyword Difficulty. Useful for finding low-KD, high-intent terms to target with collection pages.

Step 5 — Hand Everything to Claude

You now have:

AWT site audit CSV
AWT top pages CSV
AWT top backlinks CSV
GSC Queries.csv (3 months, branded filtered)
GSC Coverage notes
PageSpeed: 7 URL reports (LCP/CLS/INP + top issues)
Domain Rating: yours + 3 competitors
Backlink Checker: top 100 backlinks

Open Claude (paid plan recommended for the long context window; see do I need a paid Claude plan). Attach the CSVs. Then this prompt:

I run a Shopify store. Attached: AWT site audit, AWT top pages, AWT
top backlinks, GSC Queries (3 months, branded stripped), PageSpeed
reports for 7 key URLs, and DR comparisons vs 3 competitors.

Store context:
- Niche: [niche]
- Monthly revenue: $[X]
- AOV: $[Y]
- Site CVR: [Z]%
- Current monthly organic sessions: [N]
- My DR: [A]. Competitor DRs: [B, C, D]

I want a SEO action plan ranked by *revenue impact*, not by SEO score.
Do this:

1. TECHNICAL — From the AWT audit, find the issues that touch top-50
   revenue pages (cross-reference AWT top pages with my revenue list
   below). List them ranked by severity × revenue exposure.

2. CONTENT — From GSC, find queries where I rank position 4–15 with
   impressions > 100/mo. These are my "almost there" opportunities.
   List top 10 ranked by (impressions × CTR-uplift-potential × my CVR
   × my AOV). Show your math.

3. SPEED — From PageSpeed, name the single biggest CWV failure on a
   top-3 revenue page and the specific fix (image format, font load,
   third-party script, JS bundle).

4. AUTHORITY — Given my DR vs competitors, tell me whether content is
   even my bottleneck or whether I need links first. Be honest.

5. THE ONE THING — Rank everything from sections 1–4 together. Tell
   me the single highest-ROI fix to ship this week and the dollar
   estimate. One fix. Not three.

Top revenue pages:
[paste your top 5 product URLs and top 5 collection URLs]

Be decisive. No "consider testing." Pick.

The output is a ranked, revenue-weighted action plan. Stage 4 of the main loop is how you actually ship the fix.

What the Free Stack Misses

Honest list of what you'd pay for:

Competitor keyword research at scale. AWT only shows your own site. To pull competitor keyword lists you need Ahrefs Lite ($99/mo) or SEMrush.
Content gap analysis — "what do my competitors rank for that I don't" requires the paid tier.
Rank tracking across 100s of keywords — GSC shows actual position but only on queries that already get impressions. For a tracked keyword set, you need a rank tracker (paid).
Backlinks beyond top 100 — paid for full backlink graphs.
SERP feature tracking — featured snippets, People Also Ask presence — paid.

For a single Shopify store at <$1M revenue, the free stack is enough. Above $1M, the competitor research starts paying for itself.

Talk to Branva

We run this exact free-stack audit on every client store in the first week, then ship the fixes through the Shopify connector. Book a free call and we'll do Steps 1–5 live on your store during the call.

Frequently Asked Questions

How do I use Ahrefs for SEO audits?

Run Site Audit for technical issues (broken links, redirects, missing meta), Site Explorer for your backlink and keyword position picture, then export both and have Claude prioritize the findings by traffic impact — that last step turns a wall of issues into a ranked fix list. The exact workflow, including the free Ahrefs Webmaster Tools tier, is below.

What's the best workflow for fixing a high volume of broken internal links?

Export the full broken-links report (Ahrefs Site Audit → Internal pages → 404s), group by target URL rather than fixing one link at a time — one redirect usually fixes dozens of links — then 301 dead targets to their closest live equivalent and update high-traffic source pages by hand. We've documented the Shopify-specific version in how to fix broken links for SEO.

Is Ahrefs Webmaster Tools actually free or freemium?

Actually free for sites you verify ownership of. No card required. You get site audit, top pages, and top backlinks for your own domain. The paid tier (Ahrefs Lite, $99/mo) is for competitor research and unlimited projects.

Can I use Screaming Frog instead?

Yes — Screaming Frog (free up to 500 URLs) is a strong substitute for AWT's site audit. Pair it with GSC + PageSpeed and the prompt at Step 5 still works.

How often should I re-run this audit?

Weekly diff (the cheap version — re-run AWT audit + compare to last week) is in the main loop's Stage 5. Full audit (everything in this post) once a quarter or after any major store change (theme swap, app install, replatform).

What if I don't have Google Search Console set up yet?

Set it up first. It's free, takes 10 minutes (verify via DNS or GA), and it's the only ground-truth source for what queries Google actually shows you for. Every other tool estimates. GSC measures.

Does Claude need the audit data pasted as CSV or can I just attach the files?

Attach the files. Claude reads CSVs natively in the chat interface (paid plan). Pasting works too but eats context fast for large audits.