QB Issue Resolution:

If I understand correctly, it sounds like the deposit you recorded in your bank’s mobile app is also recorded in your books already—as long as that’s the case, we just need to edit the deposit to connect it to and close the invoice. First, let’s find the deposit in your check register.

Here’s how:

  1. Choose Accounting on the left navigation panel.
  2. Click Chart of Accounts at the top.
  3. In the Action column, select View register.
  4. Locate the correct deposit and click anywhere on it.
  5. Click Edit.

Once you’ve done that, edit the deposit by following these steps:

  1. In the Received From column, select the drop down arrow in row 1.
  2. Choose the correct Customer’s name.
  3. In the Account column, select the drop down arrow in row 1.
  4. Choose Accounts Receivable (or Trade and Other Receivables).
  5. Click Save.

Now we just need to connect the deposit to the invoice:

  1. Select the Plus (+) at the top of the screen.
  2. Choose Receive payment.
  3. Click the Customer’s name.
  4. The payment screen will now show any open invoices and credits/deposits (you may need to scroll down to see the ones you need depending on how many there are).
  5. Put a check in the boxes next to the invoice that needs to be closed and the deposit we just edited, and click Save.

That should do it! Just make sure when you are recording the payment to connect the deposit to the invoice that the amount in the Amount received box is zero (we are just connecting that deposit, we aren’t recording any additional funds received). I’ll include screenshots to show you what I mean.

Again, these steps are only if your deposit is already recorded in your books, so be sure to let me know if things are set up differently. And of course, if you have any questions, I’m always here to help.

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Resolution for Issue 'Can I accept payment after check has been deposited?' available: Yes (Solved).
Source: Intuit Community forum.

Can I accept payment after check has been deposited?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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