Deposits in QuickBooks can be removed using the Make Deposits window. When removing the deposit, the payment is removed. How Do I Delete a Deposit. It is important to record every transaction to see the inflow and outflow of the cash to your business. Duplicated entries or failed transactions can make your records go haywire. As a small and mid-sized business, maintaining records is a vital activity and it has to be conducted in an error-free way