When receiving a payment through Quickbooks online via bank transfer or credit card , does it automatically apply to the invoice ?

Thank you for posting here in Community @spitzlei-kate,

Your invoice will automatically be marked as paid. Also, the payments will be deposited into your undeposited funds.

You can create a bank deposit and apply the pending payments on the Bank Deposit screen. Let me walk you through on how to create a bank deposit in Quickbooks Online. Here's how:

1. Select the + New button.
2. Under the Others column, choose Bank Deposit.
3. From the Account drop-down▼menu, choose the account you want to deposit the money into.
4. Put a checkmark in the box for each payment you want to deposit. Use your deposit slip as a reference to make sure that the deposit total and selected payments match.
5. Select Save and Close.
   

I've also provided a screenshot for your reference.

For more details about bank deposit, refer to this link: Record and make Bank Deposits in QuickBooks Online.

In case you need help reconciling your account, check out this link: How to Reconcile an Account in QuickBooks Online.

If you have additional questions, feel free to leave a comment below. I'm always here to help. Have a great day!