Percentage-based order fees are supported on all Shopify plans, but how they’re applied depends on your plan.
Starter Plan: Percentage fees can only be applied to the order subtotal.
Growth Plan (for Shopify Plus merchants): You can apply percentage fees to either the order subtotal or the final order total.
This difference exists because Shopify Plus gives access to checkout extensions, which allow fees to be calculated after discounts on the final total. Non-Plus plans don’t have these checkout customization options, so fees are limited to the subtotal.