🔍 Overview
After resetting your Search Atlas account and reconnecting your Shopify store, you may encounter two common issues: a pixel installation error and a site audit crawler that isn't running. These issues are related — the reconnection process requires a few deliberate steps to re-establish the tracking pixel and trigger a fresh crawl. This article walks you through the full resolution process.
⚠️ Why This Happens
When you reset your account or disconnect and reconnect your Shopify store, Search Atlas loses its previous link to your site's pixel and audit configuration. The platform treats your store as a new connection and requires you to reinstall the pixel manually and initialise the site audit from scratch. Simply reconnecting the integration is not enough to restore these automatically.
✅ Step 1 — Verify Your Shopify Store Is Connected
- In the left sidebar, click Site Metrics (Site Explorer).
- Confirm your Shopify store domain appears in the site list at /site-explorer/list.
- If your store is missing, use the Add New Site option to reconnect it before continuing.
🔧 Step 2 — Reinstall the Search Atlas Pixel on Shopify
The pixel must be reinstalled manually after any account reset. Follow these steps inside your Shopify admin:
- Log in to your Shopify Admin and go to Online Store → Themes.
- Click Actions → Edit Code on your active theme.
- Open the theme.liquid file.
- Remove any previously installed Search Atlas pixel snippet to avoid duplicate code conflicts.
- Return to Search Atlas and navigate to Site Metrics (Site Explorer). Locate your site and open its settings to retrieve your unique pixel snippet.
- Paste the pixel snippet just before the closing
</head>tag in theme.liquid. - Click Save in Shopify.
Once saved, return to Search Atlas and use the Verify Pixel option (if available on your site settings screen) to confirm the pixel is detected correctly.
🚀 Step 3 — Initialise the Site Audit Crawler
After the pixel is confirmed, you need to manually start the site audit so the crawler begins indexing your store.
- In the left sidebar, click OTTO SEO → Site Audit (Site Audit).
- Select your Shopify store from the site selector at the top of the page.
- Look for the Audit Site button and click it.
- The crawler will begin running. Depending on the size of your store, the initial audit may take several minutes to complete.
You can also monitor crawl status and site health data by returning to Site Metrics (Site Explorer) in the left sidebar once the crawl has started.
💡 Tips to Avoid This Issue in Future
- Before resetting your account, note your pixel snippet and audit settings so you can restore them quickly.
- Always verify the pixel immediately after any reconnection — do not assume it carries over automatically.
- If you manage multiple Shopify stores, reinstall and verify the pixel for each domain separately.
- Clear your Shopify theme's cached files after saving the pixel to ensure the latest version is live.
🛑 Still Seeing a Pixel Error?
If the pixel verification continues to fail after following all steps above, check the following before contacting support:
- Confirm there are no duplicate pixel snippets in your theme.liquid file.
- Make sure your Shopify theme is published and active — pixel changes to an unpublished theme will not take effect.
- Disable any third-party script blockers or Content Security Policy (CSP) headers that may be preventing the pixel from loading.
If you need further assistance, open the chat widget in the bottom-right corner of the platform and type human teammate to be connected with a member of our team.