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Can’t Remove or Delete a Payment from the Make Deposits Window in QuickBooks Desktop?

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Can’t Remove or Delete a Payment from the Make Deposits Window in QuickBooks Desktop?

I’m Gary Black, and I’m running into a frustrating issue inside QuickBooks. I’ve got an incorrect payment that’s been sitting in the “Make Deposits” section, and no matter what I try, I can’t seem to delete or remove it. I didn’t intend to record it this way — it was added by mistake — but now it’s stuck in the deposit queue.

Every time I go to make a real deposit, this incorrect payment shows up as available to deposit, and it’s throwing off my totals. I’m worried it’s going to mess with my books if someone accidentally includes it in an actual deposit.

I’ve tried looking through the help articles and even attempted to void or delete it through the transaction list, but it either doesn’t respond or it’s grayed out. This is a pretty specific issue, and I can’t move forward confidently until this false entry is cleared. I need immediate guidance to delete or correct it the right way without creating a bigger accounting issue.

Hi Gary Black,

You’re not the only one stuck in this situation. Many QuickBooks users run into this exact issue where an incorrect or duplicate customer payment keeps showing up in the Make Deposits window, even when it was already handled or should no longer be there.

You’ve probably already done the basics: 

  • Looked up the transaction
  • Tried voiding it
  • Attempted to delete it through the payment list

But in some cases, the payment keeps popping back up, or the Delete option is greyed out altogether, especially when it’s linked to a deposit, sales receipt, or invoice.

When this happens, it can disrupt your workflow by inflating available deposits or causing inaccurate balances in your undeposited funds account. 

The good news? Whether you’re using QuickBooks Online or QuickBooks Desktop, you can fix this by tracing the original payment and removing it correctly.

Let’s walk you through the steps to do it right.

Why Is the Payment Stuck in the Make Deposits Window?

Possible ReasonExplanation
Payment still in Undeposited FundsThe customer payment was received but never included in a finalized deposit.
Deposit not completedYou have exited the deposit screen without saving or completing the deposit.
Duplicate or error entryAn accidental or test transaction was entered and not removed.
Payment linked incorrectlyThe payment is linked to the wrong invoice or deposit.

Steps to Delete a Payment from the Make Deposits Window

QuickBooks Desktop (Pro, Premier, Enterprise)

If the payment is showing up in the Make Deposits window and shouldn’t be there, follow these steps:

Method 1: Delete the Payment from the Customer Center

  1. Step: Open QuickBooks Desktop and go to the Customers menu.
  2. Step: Click Customer Center.
  3. Step: Find and select the customer whose payment is stuck.
  4. Step: In the Transactions tab, locate the Payment.
  5. Step: Click to open it.
  6. Step: Click Delete from the top menu (or Edit > Delete Payment).
  7. Step: Confirm deletion when prompted.

Method 2: Remove the Payment from an Existing Deposit

  1. Step: Go to Banking > Make Deposits.
  1. Step: If the Payments to Deposit window appears, click Cancel.
  2. Step: Click Previous or Next to find the deposit containing the payment.
  3. Step: In the deposit screen, locate the line with the incorrect payment.
  4. Step: Select the line and press Ctrl + Delete to remove it.
  1. Step: Click Save & Close.

Notes:

  • If the payment has been applied to an invoice, deleting it will mark the invoice as unpaid.
  • Double-check your deposit totals after removing the payment.

QuickBooks Online

You won’t see a Make Deposits window in QuickBooks Online, but the concept is similar,  payments go into the Undeposited Funds account until you create a deposit. To remove or delete the payment:

Method 1: Delete a Customer Payment

  1. Step: Go to Sales > Customers.
  2. Step: Select the customer whose payment is stuck.
  3. Step: Under the Transaction List, find the Payment.
  4. Step: Click to open it.
  5. Step: Click More at the bottom, then select Delete.
  6. Step: Confirm when prompted.

Method 2: Remove a Payment from a Bank Deposit

  1. Step: Go to Accounting > Chart of Accounts.
  1. Step: Open the bank account where the deposit was recorded.
  2. Step: Locate and open the Deposit transaction.
  3. Step: Remove the specific payment line you want to delete.
  4. Step: Click Save and close.

Notes:

  • Deleting a payment will reopen the related invoice.
  • Always verify the deposit amount after making changes.

Best Practices to Avoid This in the Future

  • Always complete the deposit after selecting payments.
  • Review the Undeposited Funds regularly to clear old or unused transactions.
  • Use Bank Deposit instead of journal entries for customer payments.
  • Set user permissions to restrict who can delete payments.

FAQs

What is the difference between deleting and voiding a customer payment in QuickBooks?

Deleting a payment removes it entirely from your books, as if it never existed. Voiding, on the other hand, keeps the transaction in your records with a $0 amount—useful for audit trails and reconciled books.

How can I tell if a payment was already included in a deposit?

Go to the “Make Deposits” window and click “Previous” to browse deposits. If the payment appears in a previous deposit, it has already been grouped with other transactions. You can also run the Deposit Detail report.

Is there a way to check who entered or last modified the payment?

Yes, in QuickBooks Desktop, press Ctrl + F to open the Find window. Locate the transaction, then click Reports > Transaction History to view audit details. In QuickBooks Online, go to the Audit Log under the Gear icon.

Can I export a list of all undeposited payments for review?

Yes, Run the Undeposited Funds report and export it to Excel or PDF. In QuickBooks Online, go to Reports > Transaction List by Date and filter for Undeposited Funds.