This happens when Shopify is not configured to treat product prices as tax-inclusive. GST Pro mirrors the tax data it receives from Shopify, so if Shopify treats prices as tax-exclusive, GST will appear added on top even if you intended the price to already include tax.
The most frequent cause is that the Shopify setting "Include sales tax in product price and shipping rate" is not enabled.
When this setting is off, tax is added on top of your product prices.
Third-party checkout tools (for example, custom or accelerated checkouts):
GST Pro works like a receipt printer.
When tax-inclusive pricing is enabled, GST Pro performs a reverse calculation — splitting the final price into taxable value and GST amount, so the total remains unchanged.
Shopify → Settings → Taxes and Duties
GST Pro → Products
GST Pro → Settings → Taxes
GST Pro cannot change what a customer was charged at checkout
Shopify tax setting changes:
GST Pro depends entirely on Shopify's Order API
The app cannot override misconfigured Shopify tax data