My clients are paying the invoices but the system is registering a payment?

Hi there Soretsky24,

It's vital that all your payments be recorded correctly in the system so that your customer balances are correct. QuickBooks Online is a great tool able to help you send invoices to your customers so they can pay you for your services. I can provide some information about payments.

If you're using QuickBooks Payments so that your customers can pay you directly from the invoice, the system automatically generates a payment transaction in the system once your customer pays so that the invoices can be correctly marked as paid.

If you're accepting the money in any other way than QuickBooks Payments, you can mark an invoice as paid by navigating to the Sales tab, then invoices. Find the invoice for which your customer paid you, then click on the option to Receive payment.

If you're receiving payments via QuickBooks Payments and they aren't being recorded as paid in your books, I recommend reaching out to the Quickbooks Online support team. They'll be able to verify your account with you in a secure setting to be able to provide some troubleshooting steps as well as notify our engineers if needed. You can contact them using one of these methods:

Schedule a Callback or start a Chat: click (?)Help in the upper right > type and enter "Contact support" into the QB Assistant > click Contact Us > explain your situation > click Let's Talk > choose Get a callback or Start a Chat. 
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if you have any other questions, feel free to reach out here.