Payments

Hello there, @lauriberzins.

Thank you for joining the Community. I'd be happy to help share some information about reconciling the invoice with a paid sales receipt in QuickBooks Online.

There are two options to record sales transactions in QuickBooks, and it depends on when you receive the payment. For a deferred payment, you can use the Invoice and Receive Payment. However, for immediate payment, you need to use Sales Receipt.

Since you got your invoice automatically from third-party software, you can use Receive Payment to know that it has been paid. To avoid duplicates, you can delete the sales receipt then you record a payment against the invoice.

Here's how to delete the sales receipt: 

1. Search and open the sales receipt.
2. Click More, then choose Void or Delete. 
3. Click Yes. 

After that, you can record the payment with the following steps:

1. At the top right, click the Plus icon.
2. Select Receive Payment.
3. Select the name of the customer, date of payment, and the payment method. 
4. Enter the amount of the payment 
5. Select the invoice to apply the payment to. 
6. Click Save.

For additional information, I've included some articles for your reference: 

• How to Record a Customer Payment
• Receive Payments in QuickBooks
• How to Reconcile an Account in QuickBooks Online

If you need to reach out for more help, our phone agents will be able to help you get to a resolution quickly. Here's how to get in touch with our Customer Care team:

1. Go to https://help.quickbooks.intuit.com/en_US/contact.
2. At the top right, select your QuickBooks version.
3. Select a topic.
4. Click on the Get Phone Number or Start a Message button.

These resources should help to get you back on track on reconciling the invoice in QuickBooks Online.

Feel free to drop a comment below if you have any other questions about reconciling the invoice or recording the payments in QuickBooks. I'd be happy to help you out. Have a great day.