Also, there's a possibility that you've received the payment into your Undeposited Funds account instead to your business checking account. In this case, you'll need to process bank deposit. To do this, you can visit this article for the detailed steps on how to Record Bank Deposits in QuickBooks Online.
If you need further assistance with the steps, I encourage you to contact our QuickBooks Online Support Team. They have additional tools to pull up your account and do a screen share.
Customer credit card payments via bill pay are not posting to my business checking account?
We are experiencing the same problem. If a customer pays their bill by clicking on the link sent with the invoice, the payment does not reduce the outstanding balance on the AR Report for weeks!!!! Any help Intuit can provide in rectifying this frustrating problem would be greatly appreciated because it makes our statements inaccurate as well.
I'll point you in the right direction for support with your concerns.
Online payments through QuickBooks Payments are deposited to your bank account automatically. Your books will auto-update as well, but since this isn't the case in your situation, I suggest you contact our QuickBooks Payments support.