Thanks for sharing your concern here in the Community, @Julian Com Serv Dist.
To give you an insight, the credit card issuer, its network, and the payments processor are all involved in charging the processing fees. Hence, QuickBooks is unable to implement the net amount of an invoice as the fees vary depending on the processor.
Also, the credit card issuer charges the merchant a commission, or a fee, for the ability to process the card for each transaction. This is why there's a fee on top of the amount.
For more insights, you can check out this article: How credit card processing works.
For future reference, read through this article: Find out when QuickBooks Payments deposit customer payments. It helps you learn more about the turnaround time to get your customer payments in your bank account.
Feel free to visit again if you have additional concerns. We're always here to help.
