Best Shopify theme audit and cleanup apps (2026)
Shopify has a growing set of apps that audit a theme or a whole store. They differ in what they check, whether they change your theme, and what the free plan includes. This page compares them side by side.
Store Health is our app. Every detail about the other apps comes from its official Shopify App Store listing as of October 2026. Where a listing does not mention a feature, the table says "Not listed", which does not mean the app lacks it. Most of these apps are new and have few or no reviews yet.
Which one fits
- Store Health: Audit & Scan: A read-only scan that covers the theme and the store data around it, with history, comparisons, and exports.
- GhostCode: Theme Cleanup: Tracing leftover code to the file and line, with malicious domain checks and script tag shutdown impact.
- ThemeSweep: Merchants who want leftovers removed for them, with a backup and 30-day undo.
- CleanTheme: A free, read-only look at the active theme with a report you can share with a client.
- StoreScan: Audit & Optimize: A broad store audit that can apply alt text, broken link, and SEO fixes for you.
- ShopAudit: SEO and Core Web Vitals checks with a checkout test and competitor benchmarks.
- Shopatch Theme Audit: Accessibility and legal checks (WCAG 2.1 AA), including draft themes.
- ThemeSafe: Security Review: Ongoing security monitoring of theme files and changes.
Theme cleanup and leftover code
| App | What it checks | Theme access | Free plan | Paid plans | Reviews |
|---|---|---|---|---|---|
| Store Health: Audit & Scan (our app) | Read-only scan of theme, scripts, products, discounts, metafields, files, links, and AI visibility | Read-only | 4 preview scans (overall score and problem count), no credit card | Monthly $19.99/month, Yearly $199.99/year | 8 (5.0 stars) |
| GhostCode: Theme Cleanup | Theme cleanup and leftover code tracing | Read-only | First scan, then 1 per month, one theme, preview of the top finding only | Standard $9/month, Professional $29/month (unlimited scans, auto-scan when a theme is published, scan comparison) | 0 |
| ThemeSweep | Finds and removes leftover app code | Changes the theme (with approval, on a copy) | Free plan available | Starter $9.99/month, Pro $19.99/month, Agency $39.99/month | 0 |
| CleanTheme | Read-only scan of the active theme | Read-only | Free | None listed | 0 |
Store Health: Audit & Scan
Checkpoint · Launched February 2026 · Reviews: 8 (5.0 stars)
- Scans eight areas in one pass: theme code, scripts, products, discounts, metafields, files, navigation links, and AI visibility
- Script tags and renders of missing snippets shown with file and line number
- Metafield analysis: unused, empty, and theme-referenced metafields
- Saved scan history and side-by-side compare
- Scheduled scans and email reports
- Live Signals: where shoppers drop off after add to cart, at checkout, or on a form error, by device
- Exports: PDF and JSON
Free: 4 preview scans (overall score and problem count), no credit card. Paid: Monthly $19.99/month, Yearly $199.99/year.
GhostCode: Theme Cleanup
Alpenglow Software LLC · Launched April 2026 · Reviews: 0
- 30+ checks across 8 areas and 100+ app signatures
- Traces each finding to the file, line, and snippet
- Flags malicious script domains
- Shows apps affected by the script tag shutdown (March 1, 2027)
- Weekly mobile speed report per app
- View-only permissions
Free: First scan, then 1 per month, one theme, preview of the top finding only. Paid: Standard $9/month, Professional $29/month (unlimited scans, auto-scan when a theme is published, scan comparison).
GhostCode: Theme Cleanup on the Shopify App Store · Store Health vs GhostCode
ThemeSweep
JMS Dev Lab · Launched September 2026 · Reviews: 0
- Finds JS, CSS, and Liquid left by uninstalled apps, plus orphaned files
- Links each finding to the app it came from
- One-click cleanup: delete or comment out
- Full backup before cleanup and 30-day undo
- Changes the theme, with approval, on a copy of the theme
Free: Free plan available. Paid: Starter $9.99/month, Pro $19.99/month, Agency $39.99/month.
ThemeSweep on the Shopify App Store · Store Health vs ThemeSweep
CleanTheme
CleanTheme Apps · Launched May 2026 · Reviews: 0
- Old snippets, tracking pixels, external scripts, and app extension references
- File, line, and a confidence score for each finding
- Client-ready report
Free: Free. Paid: None listed.
General store and theme audits
| App | What it checks | Theme access | Free plan | Paid plans | Reviews |
|---|---|---|---|---|---|
| StoreScan: Audit & Optimize | Broad store audit with fixes | Not listed | SEO only, 2 scans per month | $9.99, $19.99, and $49.99 per month | 0 |
| ShopAudit | SEO, speed, and conversion checks | Not listed | 20 pages, 1 audit per month | $19, $49, and $99 per month | 0 |
| Shopatch Theme Audit | Accessibility and legal checks | Read-only | Free plan available | Watcher $20/month | 0 |
| ThemeSafe: Security Review | Theme security | Not listed | Daily scan, 250 files | $19 and $49 per month | 7 (5.0 stars) |
StoreScan: Audit & Optimize
Glavient · Launched January 2026 · Reviews: 0
- 9 to 10 scanners: setup, SEO, speed, security, accessibility, broken links, inventory, analytics, images
- Health score
- AI recommendations
- One-click fixes for alt text, broken links, and SEO
Free: SEO only, 2 scans per month. Paid: $9.99, $19.99, and $49.99 per month.
ShopAudit
FEDELI · Launched June 2026 · Reviews: 0
- SEO, Core Web Vitals, images, broken links, price and stock, checkout test
- Scores in 5 categories
- AI fixes for meta tags and alt text
- Competitor benchmarking
Free: 20 pages, 1 audit per month. Paid: $19, $49, and $99 per month.
Shopatch Theme Audit
Shopatch · Launched September 2026 · Reviews: 0
- WCAG 2.1 AA, contrast, alt text, and keyboard checks
- File and location for each finding
- Includes draft themes
- Read-only
Free: Free plan available. Paid: Watcher $20/month.
ThemeSafe: Security Review
galaxy team · Launched December 2025 · Reviews: 7 (5.0 stars)
- Scans the theme for suspicious scripts and unsafe code
- Change monitoring
- Security alerts
Free: Daily scan, 250 files. Paid: $19 and $49 per month.
FAQ
Which Shopify audit apps find leftover app code?
GhostCode, ThemeSweep, CleanTheme, and Store Health all look for code left behind by uninstalled apps. ThemeSweep can also remove it for you, while the other three are read-only.
Do theme audit apps change my theme?
Most apps on this list say they are read-only. ThemeSweep changes the theme with your approval, on a copy, with a backup and 30-day undo. StoreScan and ShopAudit offer one-click or AI fixes for things like alt text and SEO fields.
Is there a free Shopify theme audit app?
Every app here has a free option. CleanTheme is free, ThemeSafe's free plan scans daily up to 250 files, Store Health includes 4 preview scans, and the others limit the number of scans or what the free plan shows.
How was this comparison made?
Every competitor detail comes from that app's official Shopify App Store listing, as of October 2026. When a listing does not mention a feature, we write "Not listed" instead of assuming it is missing. Store Health is our app.
Try Store Health for free
4 preview scans, no credit card. Read-only, so nothing in your store changes. See also the app removal guides and the free Shopify audit.