Shopify Theme Updates and Custom Code Handling in 2024-2025

Shopify's theme update system fundamentally replaces all theme files during updates, meaning custom code modifications are lost unless they don't conflict with the update. This core limitation affects both paid and free themes, though paid theme developers have created sophisticated solutions to address these challenges. The system has evolved significantly with Online Store 2.0 architecture and major changes are coming in 2025.

The update process follows two paths: automatic updates for unmodified themes (preserving only theme editor settings) and manual updates for modified themes (requiring merchant review). Custom snippets in the /snippets/ folder are not specially protected and get overwritten during updates if they conflict with theme changes, contrary to common developer assumptions.

How theme updates work for paid vs free themes

Free Shopify themes like Dawn use a streamlined automatic update system that only works with unmodified code files. These updates include bug fixes and security patches but no functional changes. The system preserves theme editor customizations (colors, fonts, section settings) automatically but completely replaces any custom code modifications. Around 90% of Dawn users run outdated versions specifically because code modifications prevent automatic updates.

Paid themes from major Theme Store partners like Archetype Themes, Pixel Union, and Out of the Sandbox follow a more sophisticated manual update process. All paid theme updates create an unpublished copy in the merchant's theme library with an "Updated copy of" prefix. Theme developers must follow minimum 4-week intervals between updates and use semantic versioning. The key difference is that paid theme developers have created an ecosystem around the Theme Updater app, which uses AI-powered code analysis to attempt preservation of custom modifications during updates.

The fundamental technical difference is that free themes rely entirely on Shopify's built-in system, while paid theme developers have built professional services and tooling to handle custom code migration challenges.

What happens to custom snippets during theme updates

Custom snippets face the same preservation rules as all other theme files during updates. Snippets in the /snippets/ folder are NOT automatically preserved and will be overwritten if they conflict with theme updates. This is a critical misconception in the developer community.

During the update process, Shopify's system checks all files except settings_data.json and JSON files in the templates directory. Custom snippets are preserved only if they don't conflict with the incoming theme changes. When conflicts occur, merchants receive a "Theme added: code edits could not be included" notification, and all conflicting custom code must be manually reapplied to the new theme version.

JSON-LD snippets are particularly vulnerable because they're typically stored in the snippets folder and require manual recreation after updates. Developer communities increasingly recommend moving from custom JSON-LD snippets to app-based implementations using App Embeds, which survive theme updates.

Shopify 2.0 themes vs older themes regarding updates

Online Store 2.0 themes benefit from superior update architecture with JSON templates supporting sections on all pages, dynamic sources, and modular section-based structure. This architecture provides better separation of content from code structure, improving update compatibility and enabling more granular control over what gets updated during theme modifications.

The section-based architecture allows for more targeted changes during updates, with better preservation of merchant customizations through enhanced theme app extension compatibility. JSON templates provide merchants with greater layout flexibility while maintaining better update safety.

Legacy/vintage themes have significantly more limited update mechanisms with higher likelihood of custom code conflicts. Shopify's free vintage themes now receive only security fixes, and the company officially recommends migrating to Online Store 2.0 themes for better long-term update compatibility and access to latest Shopify features.

The technical benefits of Online Store 2.0 include support for Theme Blocks (reusable components), enhanced metafield integration, and better app integration through App Blocks, all of which reduce the need for custom code modifications that cause update conflicts.

Best practices for preserving custom code during updates

The developer community and Shopify's official documentation converge on several critical practices. Always duplicate your theme before making any updates to create a backup copy. Document all custom modifications comprehensively with clear naming conventions and prefixes for custom files to make them easily identifiable during migration.

Version control strategies from experienced developers include implementing Git-based workflows with three-branch systems (main, dev, theme-update), using upstream remotes for theme developer repositories, and maintaining separate source and compiled code repositories. Professional development shops use build tools like Webpack with pre-commit hooks running Theme Check for error detection.

For JSON-LD and structured data preservation, the community strongly recommends moving from hard-coded snippets to app-based solutions using App Embed blocks. Apps with App Block integration survive theme updates, while custom code modifications in theme files are lost.

Testing strategies include always testing updates on duplicate or development themes first, using online diff tools like Diffchecker.com to compare theme versions, and budgeting developer time for manual code migration in project timelines.

How paid theme developers handle updates differently

Major paid theme developers have created a sophisticated ecosystem to address Shopify's custom code preservation limitations. The Theme Updater app, developed by Out of the Sandbox and supporting partners like Pixel Union, Archetype Themes, and Clean Canvas, represents the industry's primary solution for automated custom code preservation.

This app uses AI-powered code analysis to identify and migrate custom modifications during theme updates, creates color-coded merge conflict comparisons, and provides both free and paid tiers of update assistance. The Pro plan includes customization preservation features that attempt to transfer custom code when possible.

Professional support structures differentiate paid themes significantly. Paid theme developers provide lifetime updates, dedicated support channels, comprehensive documentation, and integration with Shopify Expert networks for complex customizations. They offer multiple update options: manual updates for modest customizations, Theme Updater app integration, and professional services through Shopify Experts.

In contrast, free themes provide only basic Shopify Support for simple changes and community forums for assistance, with no custom update services or professional code migration support.

Whether custom snippets get overwritten during updates

Yes, custom snippets in the /snippets/ folder get overwritten during theme updates if they conflict with incoming theme changes. This represents one of the most common misconceptions in Shopify development, with many developers incorrectly assuming snippets have special protection.

The technical process works by replacing all theme files that conflict with updates, including custom snippets. Snippets are preserved only if they remain compatible with the new theme version and don't conflict with any updated functionality. When conflicts occur, the entire conflicting file is replaced, not just the conflicting portions.

Naming strategies can improve preservation chances: using distinctive prefixes for custom snippets, maintaining consistent naming conventions, and keeping custom snippets completely separate from theme core functionality. However, these strategies don't guarantee preservation – they simply make manual migration easier when conflicts occur.

Recent changes to Shopify's theme management system

Major Theme Store redesign launches July 2025 with submission requirements effective May 15, 2025. This includes new theme zip structure requiring /listings folder for preset management, industry categorization across 20 categories, and enhanced submission forms. Critical deadline: Theme developers must resubmit by June 22, 2025 to maintain their listings.

Technical breaking changes include BOOMR JavaScript library deprecation by January 31, 2025, requiring migration to window.Shopify.theme properties. Font system updates mandate deprecated font replacement by January 3, 2025, with automatic replacement starting August 2025.

Enhanced development tools rolling out through 2024-2025 include comprehensive code editor improvements with full LiquidDoc integration, search functionality across theme files, multiple editor themes including dark mode, and enhanced Theme Check linter integration. The new LiquidDoc system provides JSDoc-inspired documentation for snippets with structured parameter definitions and real-time validation.

Revenue changes starting January 1, 2025 implement 15% revenue share on all Theme Store earnings, eliminating the previous 0% subsidy for earnings under $1M USD. Enhanced anti-piracy measures with license detection were implemented in July 2024.

Conclusion

Shopify's theme update system prioritizes merchant experience and security while creating significant challenges for custom code preservation. The fundamental architecture replaces theme files during updates, making backup and documentation strategies essential rather than optional.

The division between free and paid themes has created a two-tier ecosystem: free themes rely on Shopify's automatic update system that only works with unmodified files, while paid theme developers have built sophisticated professional services around the Theme Updater app to handle custom code migration.

The 2024-2025 changes represent Shopify's push toward more standardized, maintainable theme development with enhanced tooling and stricter requirements. Success requires adopting update-safe development practices, leveraging Online Store 2.0 architecture, and understanding that custom code preservation remains a professional service rather than an automated feature.