Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

Hello, we're working in QBO and have a situation where a customers check was received by a partner and remotely direct deposited into our bank account. However, that check was incorrectly added to QBO via an electronic download from our bank and was never applied to the customer's invoice. Months have gone by and we need to figure how to apply the now reconciled deposit against the customer's outstanding invoice? Do we simply create a credit memo and apply it or is it necessary to create some type of journal entry? Any advice would be appreciated. Thanks!

Best answer January 26, 2018
Best Answers ‎January 26, 2018 07:47 AM

Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

You've come to the right place, I'd love to help apply the deposit to the invoice to remove the outstanding balance.

Let's first locate the deposit, here's how:

  1. Click Accounting on the left panel.
  2. Locate the bank account where the payment was direct deposited into, then click View register .
  3. Locate the deposit and click it.
  4. Click Edit .

After that, let's link the deposit to the invoice. I'll walk you through:

  1. Select the customer from the Received From column.
  2. Select Accounts Receivable from the Account column.
  3. Click Save and close .
  4. Click the plus (+) icon.
  5. Select Receive Payment .
  6. Select the customer.
  7. Place a check next to the invoice and deposit.
  8. Click Save and close .

Now, the invoice is marked as paid. I've added this article for your future reference: Linking a Deposit to an Invoice

Thanks for giving me the opportunity to help. I'm here anytime to need further assistance with QuickBooks Online.

31 Comments 31 ‎January 26, 2018 07:47 AM

Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

You've come to the right place, I'd love to help apply the deposit to the invoice to remove the outstanding balance.

Let's first locate the deposit, here's how:

  1. Click Accounting on the left panel.
  2. Locate the bank account where the payment was direct deposited into, then click View register .
  3. Locate the deposit and click it.
  4. Click Edit .

After that, let's link the deposit to the invoice. I'll walk you through:

  1. Select the customer from the Received From column.
  2. Select Accounts Receivable from the Account column.
  3. Click Save and close .
  4. Click the plus (+) icon.
  5. Select Receive Payment .
  6. Select the customer.
  7. Place a check next to the invoice and deposit.
  8. Click Save and close .

Now, the invoice is marked as paid. I've added this article for your future reference: Linking a Deposit to an Invoice

Thanks for giving me the opportunity to help. I'm here anytime to need further assistance with QuickBooks Online.

‎April 23, 2018 07:51 AM

Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

Thanx for the answer. I have a follow-on question. We pay sales commission based on the cash receipts. In the above scenario let's assume an invoice is dated in January, the cash was ACTUALLY received in March, but not credited to the invoice until July. I am concerned that the system will (despite the books being long closed for March) record this as a cash sale in March. How do I get this 'fix' to show the cash sale in July; the month the issue was resolved?

‎April 23, 2018 02:33 PM

Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

I’m glad to share how QuickBooks Online (QBO) reports the sales once you receive the invoice payments.

QBO reports the sales based on the accounting method of the company. If you’re set up for Accrual method, the sales are recorded at the time you enter the invoice regardless of whether it’s paid or not.


Cash method reports the sales at the time you receive payments. It doesn’t matter whether the payments have been deposited to the bank account or not.

In the scenario above, the cash sales will be reported in March if you select Cash method. You’ll see the sales posted in January when you select Accrual .

To show the cash sales in July, you’ll have to set the payment date to this specific month. Then, run the sales report in Cash accounting method.

I’ve added some examples in the screenshots below.

I also recommend consulting an accountant before making any changes to the invoices or payments. We need to ensure the books are still accurate since they were already closed last March.

Don’t hesitate to let me know if there’s anything else you need. You can mention my name (@MichelleT) if you have additional questions, and I’ll be sure to get back to you.

‎May 01, 2018 11:06 AM

Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

I would love this answer for the desktop version, which does not have an 'Accounting' option in the left sidebar.

‎October 11, 2018 11:44 PM

Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

When I follow the steps outlined in your first 4 steps QB says I should "receive payment" first. Im confused?

Not applicable ‎October 30, 2018 08:17 AM

Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

I have two direct deposit payments that were applied to the invoices and show up on my bank statement but not in my check register. Because of this I cannot reconcile my bank account. Why would this happen?

‎December 30, 2018 06:17 AM

Payment received, deposited to bank account but not applied to invoice - how to correct afterwards?

I tried following your instructions however, it gave me the RED are you sure you want to do this because you've already reconciled message.

I have this issue for all of 2018 so I need to figure out how to fix all the deposits so the Customer Account balances are accurate. I already show the Customer in the Received From column and I show Consulting Income in the Account column. I'm guessing that with the auto download transactions from a bank account that you still need to receive payments first before accepting the deposits, even though you select the customer in the Received From column. Anyways. I also don't know where the plus (+) icon is that you are referring to ~ it sounds like it might open a Receive Payment option?

Is it even possible to correct these after the bank account has already been reconciled, without throwing off balances? If not, maybe I can do journal entries to fix it? My client's previous QB account had decades of information in it and it was throwing off tax returns so I went in and recreated the entire year for 2017 and was hoping to start clean but now I have this deposit issue. Any advice you can give me would be greatly appreciated!!