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Level 2

Receive online payments on invoice

I received the payments from online payments (the ones we sent with the pay now button), but when I download the payments I can record the deposits, but my invoice is still with a balance due, how do apply the payment to the invoice.
What is the procedure to link the payment from the customer to the invoice?

QuickBooks Team

Receive online payments on invoice

I can walk you through in applying the deposit to the open invoice, idamar1. 


We can either automatically match the deposit from your bank feeds to the customer's invoice. We'll just have to turn this feature on and we do the matching for you. 


Here's how: 

  1. From Banking menu, select Record Merchant Service Deposits.
  2. Click Change your deposit settings.
  3. Turn on the Auto match & record setting.
  4. Select Save.

If you want to manually do it in which you can further review the deposit and invoice it'll be matched, you can refer to this article: Automatically record QuickBooks Payments bank deposits. For more information about deposits for your QuickBooks payments services, here are a few references:

Feel free to leave your reply if you need more help. Take care always!

Level 2

Receive online payments on invoice

Hi Catherine, thank you for your response

what I mean is that I already can make the setup of the online payments.

What I want to know is why I can't see the current deposits on the get online payment section

it says:

Merchant Service Deposits is sorted.
There are no transactions to record
and I supposed to have transactions to record from April and May 2020
how do update this information?
QuickBooks Team

Receive online payments on invoice

Hello, @idamar1


Try to check if you have updated your QuickBooks Desktop to its latest release. This will keep your software up-to-date and have the latest features and fixes. 


To update it manually:


  1. Close your company files and QuickBooks and then go to the Windows Start menu.
  2. Right-click the QuickBooks icon and select Run as administrator.
  3. From the No Company Open screen, go to the Help menu and select Update QuickBooks Desktop.
  4. In the Options tab, select Mark All and then click Save.
  5. Go to the Update Now tab and select the Reset Update checkbox.
  6. When you're ready, select Get Updates.

See this article for more information: Update QuickBooks Desktop to the latest release. If the transactions from April and May are still not showing, then I suggest reaching out to our Payment Support team.


They can take a look into your account and trace those transactions. You can get their phone number through this link: Contact Payments Support


Also, here’s more information on how we handle deposits and payments: Automatically record QuickBooks Payments bank deposits


Let me know if there's anything that I can help. I'm always here to assist. Have a great rest of the day!

Level 2

Receive online payments on invoice

Hi Mary,

I already updated QuickBooks

I still have the problem, 

I do see the transactions on the merchant service center, but when I am trying to link (match) the online payments received and create the deposits I don't see the information.

When I click on the button Get Online Payments> Virtual > I do not see any deposit to record


QuickBooks Team

Receive online payments on invoice

Hello, @idamar1.

Let me route you to the best available support so we can further investigate the root cause of why your deposit transactions are not imported in QuickBooks.


Since the Community is a public forum, I'd recommend contacting our Merchant Support team. They have the tools to trace the integration between your QuickBooks software and your Merchants account. 


Here's how:

  1. Go to:
  2. Locate QuickBooks Desktop with Payments.

Let me know how your call goes. I am always here to help you if you have other questions handling customers' payments in QuickBooks.  

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