Deposits in QuickBooks can be removed using the Make Deposits window. When deleting the deposit in QuickBooks, the payment is removed as well if you are using the Undeposited Funds account. If you plan to deposit the funds at a later time, you must also recreate the original payment. If you are not using the Undeposited Funds account and plan to make the deposit later, you can leave the original payment for the deposit intact. Otherwise, you must be sure to manually delete the payment as well.