This guide outlines the validated, production-ready process to install the OTTO Pixel on Shopify websites using the updated Search Atlas (AI SEO) interface.
This ensures OTTO’s diagnostic engine can properly detect your Pixel, activate automation, and deploy SEO fixes across your entire Shopify store.
⚠️ This method has been verified across multiple Shopify builds (Online Store 2.0 themes, legacy themes, and custom layouts).
📄 Step 1: +Create a new project.
📄 Step 1: +Create a new project.
Start inside your Search Atlas dashboard.
Instructions:
Left Sidebar → AI SEO → All Sites → + Create (top-right)
Follow the Setup Steps
🌐 Step 2: Select or Add Your Website
🌐 Step 2: Select or Add Your Website
Enter your full Shopify URL (e.g.,
https://yourstore.com).Wait for the green verification checkmark.
Click Continue.
📝 Step 3: Set up Fields (Optional)
📝 Step 3: Set up Fields (Optional)
You will see fields for Business Information, Address, and Social Profiles.
• These fields are optional for Pixel installation.
• You may complete them now or later.
Click "Continue" to proceed.
📎 Step 4: Copy Your OTTO Pixel Script
📎 Step 4: Copy Your OTTO Pixel Script
Inside the Installation Guide:
Select Shopify from the CMS options.
Click the Video Guide Card, then scroll to Pixel Code.
Click Copy to copy your OTTO Pixel
<script>.(Optional) Click Email My Developer to send the snippet.
Click "Step by step" for detailed Shopify instructions (See the next step).
Click "Continue" in the bottom right corner.
✋ Stop here — now switch to your Shopify dashboard to insert the script.
🛠️ Step 5: Add the Code in Shopify
🛠️ Step 5: Add the Code in Shopify
Open your Shopify Admin Dashboard.
In the left-hand menu, go to Sales Channels > Online Store.
Click Themes.
Locate your active/live theme, then click the three-dot menu (⋯) "Customize" next to it.
Select Edit Code.
Insert the Script into theme.liquid
In Shopify’s code editor:
On the left sidebar, locate the Layout folder.
Open the file named theme.liquid (note: the name may vary slightly depending on your theme, but it will usually be “theme.liquid” in the Layout folder).
In the code, find the <head> tag near the top.
Paste the script directly under <head> and before any other code
Click Save.
⚠️ Important Clarification
The Pixel must be:
In the global theme.liquid
Inside the <head>
Near the top of the head for the earliest loading
On the active published theme, not an unpublished one
Applied site-wide, not inside a single template or section
This guarantees OTTO can detect the Pixel across all pages of your Shopify store.
7. In the file structure, find and open your theme.liquid file.
8. Scroll to the <head> section and paste the OTTO Pixel right before the closing </head> tag.
9. Click Save in the top-right corner.
✅ This ensures the OTTO Pixel is embedded across your entire site.
🔍 Step 6: Verify Installation in Shopify
🔍 Step 6: Verify Installation in Shopify
Open your website.
Press Ctrl+U (View Page Source).
Use Ctrl+F to search for Ctrl+U UUID.
If found, the pixel is installed.
Now, return to the Search Atlas dashboard!
🚀 Step 7: Activate in SearchAtlas
🚀 Step 7: Activate in SearchAtlas
Confirm your Shopify site is live.
Once OTTO finishes initializing your project, your site appears inside:
AI SEO → All Sites
Click your project to open it.
You’ll see:
Your domain
Healthy Pages
OTTO Grader
Content / Authority / Technicals / UX pillars
On the right:
A red label → “Not Installed” / “OTTO Not Found”
A Scan button
A yellow/orange Disengaged toggle
Next Steps
1️⃣ Click Engage OTTO (Click the toggle button when it's disengaged)
→ This prepares your site for Pixel verification.2️⃣ Click Scan
→ This opens the Installation Diagnostics modal.Your domain appears automatically.
3️⃣ Click Run Diagnostics
→ OTTO checks your Shopify store for Pixel placement.A message appears:
“Running Diagnostics… We’re checking the selected page for any OTTO implementation issues.”
Please wait a few moments (it can take a couple of minutes).
⏳Once the san is finished, If it still shows red:
Wait 3–5 minutes for Shopify to propagate theme updates → then refresh the dashboard and rerun the scan.
Once detected, the status updates to green (“OTTO Engaged”).
That’s it! The OTTO Pixel is now live on your Shopify store, powering automated insights and performance boosts for your SEO strategy. Make sure to revisit the diagnostics panel anytime to ensure your tracking is running smoothly.
🔎 Understanding Your OTTO Installation Diagnostics Results
OTTO runs several validation checks. Here is what each status means:
❌ 1. OTTO not detected
❌ 1. OTTO not detected
Pixel not found.
Fix: reinstall in theme.liquid above </head>.
❌ 2. Incorrect UUID
❌ 2. Incorrect UUID
Pixel is installed but belongs to a different project.
Fix: replace with the correct UUID from the Installation Guide.
⚠️ 3. Duplicate Installation Detected
⚠️ 3. Duplicate Installation Detected
Multiple Pixels found:
Script added twice in theme.liquid
Script added via an app + manual install
Pixel in both theme.liquid, and app embed
Fix: remove duplicates → leave one Pixel.
🟡 4. OTTO is disengaged
🟡 4. OTTO is disengaged
Pixel found but not active.
Fix: toggle the button located on the left side of the word "Disengaged" to Engage OTTO and then Run Scan.
🟢 5. Deploys Verified — OK
🟢 5. Deploys Verified — OK
On-page SEO fixes were found in your live HTML.
→ No action needed.
⚠️ 6. Some deployments are not identified
⚠️ 6. Some deployments are not identified
Fixes deployed by OTTO weren’t found in the live Shopify HTML.
Common causes:
Shopify theme caching
CDN (Cloudflare) is serving the old version
Theme not published
Multiple themes active
Fix: publish → clear cache → re-run Scan.
🟣 7. Purple Banner (first-time installs)
🟣 7. Purple Banner (first-time installs)
You may see:
“Site processing is still in progress.”
“Waiting for data…”
“Pixel detected — awaiting first scan results.”
This is normal!
OTTO’s first crawl can take up to 24 hours.
If more than 24 hours pass:
Go to Scan → Run Diagnostics → Re-run Crawl.
📊 Summary Table
📊 Summary Table
Message | Meaning | Action |
❌ OTTO not detected | Pixel missing | Install Pixel, wait 2–5 min |
❌ Incorrect UUID | Wrong project Pixel | Replace with the correct UUID |
⚠️ Duplicate Installation | More than one Pixel | Remove duplicates |
🟡 OTTO disengaged | Pixel found but inactive | Engage OTTO |
🟢 Deploys Verified | Fixes OK | No action needed |
⚠️ Deploys Missing | Fixes not found | Clear cache → rescan |
🟣 Processing banner | First crawl running | Wait up to 24 hours |
With the OTTO Pixel successfully installed and verified on your Shopify store, your site is now fully connected to Search Atlas’s AI-powered SEO engine. From this point forward, OTTO can crawl your pages, detect technical issues, apply automated optimizations, and monitor ongoing improvements across your entire domain.
If you ever update your theme, publish a new layout, or install additional scripts, re-run a Diagnostic Scan to confirm everything remains properly connected. Your Shopify site is now ready to benefit from continuous SEO enhancements, real-time insights, and fully automated optimization workflows.