I prefer to be paid using my own system to avoid the 2.99% fee. How do I turn off the QuickBooks payment function when I send invoices?

It's great having you here in the Community for assistance @vaviola. I'm here to help you with how you can disable the payment option for invoices.

Here's how:

1. Go to the Gear icon menu.
2. Choose Accounts and Settings.
3. Move over to the Sales menu and click the Pencil icon for Invoice payments.
4. In the Payment options section, uncheck the box for Accept Credit Cards.
5. Click Save and Done.

For more detailed information on this process, check out the QuickBooks Online section outlined in this help article: Add or modify the accepted credit card types in QuickBooks.

Moreover, you can record invoice payments in two ways. To know more about this, I've added this article for your reference: Record Invoice Payments In QuickBooks Online.

If you have further questions about managing your transactions in QBO, feel free to reply. I'm always here to lend a hand.