Yes — you can absolutely add custom code to themes built from scratch using the Atlas theme builder, just like you would with any compatible Shopify theme.
Atlas-built themes are fully compatible with:
Custom HTML, CSS, and JavaScript
Custom Liquid blocks
Third-party scripts like tracking pixels, widgets, or integrations
Limitations with Third-party Themes
Atlas does not support the modification or customization of third-party themes purchased externally, including those from the Shopify theme store. To utilize Atlas, you must create a new theme using the Atlas store builder instead of modifying a pre-existing one. This ensures compatibility with Atlas's unique tools and capabilities.
How to add custom code
1. Using the Shopify theme editor (no coding required):
Go to Online Store > Themes > Customize
Inside of any Atlas theme section you can scroll down to the bottom and open the "Custom CSS" tab
Paste in your embed code, widget script, or custom code
2. Editing the theme files directly:
Go to Online Store > Themes
Click Actions > Edit code
From here, you can modify:
theme.liquidproduct.liquid,collection.liquid, etc.Any custom CSS or JS files
Best Practices
While Atlas support focuses on assisting with issues and bugs directly related to Atlas-designed themes, the team does not offer custom design services. For advanced custom design needs, such as creating new theme sections or replicating designs from other sites, consider enlisting the services of a Shopify developer.
Always duplicate your theme before making edits
Be cautious when editing core layout files — one missing bracket can break the layout
For advanced use cases (like animations or checkout integrations), consider working with a Shopify developer
tip: If you’re not comfortable editing theme code, we recommend using the Custom Liquid block to safely insert scripts or embeds without risk. If your customization needs exceed the scope of Atlas's capabilities or your expertise, hiring a Shopify developer is strongly recommended for advanced modifications.
Let me know if you’d like this cross-linked under the customization section as well.