Quickbooks has my correct checking account balance after a payment was made, but the QuickBooks balance doesn't reflect the customer's payment.

Thanks for reaching out to us here in the Community, garrett1.

I’m here to provide clarification why the QuickBooks Online balance and your actual bank balance don't match.

This could happen for a few different reasons. For example, there may be duplicate or edited transactions, outstanding checks or new transactions for a connected account.

Feel free to read this article for more information: How to fix differences between QuickBooks balance and bank balance.

To resolve this, match the invoice to the deposit. This process will make your bank register balance match to the actual bank balance.

Here’s how:

1. Go to Banking on the left panel.
2. Select the Banking tab.
3. Choose the specific transactions in the For Review tab.
4. Double-click on the transaction to expand it.
5. Click on Find match.
6. In the Match transaction page, choose the transaction that exactly matches with the deposit.
7. Click Save.

For more information about the process, check out this article: How to add and match downloaded banking transactions.

After following these steps, your financial records are in tiptop shape. 

Stay in touch if you have additional questions about QBO. I'm always here to answer them for you. Wishing you the best.