This happens when order-level discounts are not distributed across individual line items. By default, GST Pro calculates tax on the original product price unless the setting to split order discounts into line items is enabled.
When a discount is applied to the entire order (for example, a ₹100 discount on the cart):
GST Pro needs explicit permission to distribute the discount across products.
GST Pro calculates tax based on what Shopify sends in the order data.
When discount splitting is enabled, the ₹100 discount is distributed across items, each item's taxable value is reduced, and GST is calculated only on the final amount paid.
GST Pro → Settings → Taxes
Once enabled:
GST Pro cannot modify what the customer paid at checkout
If Shopify order data does not include a discount:
Discounts created entirely outside Shopify:
Tax calculation depends on: