Shopify apps integrate with themes differently depending on when they were built. Most modern Shopify apps use Theme App Extensions, which include App Embeds and App Blocks. These integrations don’t modify your theme files directly and can usually be enabled, disabled, or removed without leaving code behind.
However, some older apps or apps designed to work with legacy themes may still inject Liquid, JavaScript, CSS, or snippets into your theme. If those changes aren’t fully removed when the app is uninstalled, they can sometimes cause theme issues or affect storefront performance.
How modern Shopify apps integrate with themes
Most apps installed on Online Store 2.0 themes use Theme App Extensions, which provide a safer way to add storefront functionality.
There are two common types:
App Blocks
App blocks appear as blocks inside the Theme Editor and can be added, moved, or removed without editing theme code.
Examples include:
- Size charts
- Product reviews
- Upsells
- Product badges
App Embeds
App Embeds are enabled from:
Online Store → Themes → Customize → App embeds
Unlike app blocks, app embeds aren’t placed inside a section. Instead, they can:
- display floating widgets (chat, reviews, accessibility tools)
- inject JavaScript or CSS
- load tracking scripts
- add storefront functionality behind the scenes
Since app embeds are managed by Shopify, disabling the toggle usually removes the app’s functionality without modifying your theme files.
Because Shopify now encourages apps to use Theme App Extensions instead of directly modifying theme files, leftover code is less common than it was previously.
However, stores that have used older apps, legacy themes, or apps that still inject custom code may still contain leftover Liquid, JavaScript, CSS, snippets, or template modifications after an app has been removed.
Troubleshooting third-party app code and integrations
Note: Pixel Union supports the default functionality of its themes but doesn’t provide support for third-party apps or custom code added by those apps. If an app requires installation, configuration, or removal of custom integrations, please contact the app developer directly.
Contact the app developers
App developers are best equipped to confirm how their app integrates with your theme.
They can also confirm whether the app uses:
- App Embeds
- App Blocks
- Theme file modifications
- Custom Liquid or script injection
If manual cleanup is required, they should be able to identify which changes can be safely removed.
App developers can be contacted through the App Store.
Compare theme files to the default theme
Comparing theme files is most useful when troubleshooting apps that modified the theme’s Liquid files directly. Apps that use Theme App Extensions generally don’t require manual comparison because their functionality is managed through Shopify rather than embedded into your theme files.
Get the default copy for comparison
Use the Theme Updater for installing a default copy of the latest theme version.
Compare to your theme files
Use a tool like Diff Checker to compare your theme files. Theme files can be accessed by going to Actions > Edit code in your Online Store's Themes.
Start fresh with the latest theme version
Starting with a fresh copy of the latest theme version is often the quickest way to eliminate legacy app code and outdated customizations.
To complete this task, add a blank copy of the latest version to your store:
Use Theme Updater to access the latest version
After installing the new theme:
- reinstall only the apps you still use
- re-enable any required App Embeds
- add any necessary App Blocks
- allow each app developer to reinstall any required integrations
This helps avoid carrying over unused code from apps that are no longer installed.
Then contact the app developers of the apps you need to keep. They can confirm the installation steps needed for the new version. Once this is complete, add your content and adjust your settings to match your previous storefront.
Get hands-on help with app code
You can get a Shopify Expert to investigate leftover app code. We recommend Storetasker!