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Record QuickBooks payments deposits & fees in QuickBooks Desktop

For entering deposits and fees in QuickBooks Desktop software for Windows, follow the steps below. (these steps are not for QuickBooks 2015, to see those steps click here HOW25254)

Detailed instructions

If this is the first time or if this is a newly restored company file, you will need to select the appropriate bank and fee accounts in QuickBooks. Click the link below for more information.


Download Your Merchant Service Deposits and Fees

1. In QuickBooks, choose Banking > Make Merchant Service Deposits.

2. Click  (Make/Record) Merchant Service Deposits.

3. A window appears displaying all downloadable deposits and fees.

       Merchant deposits and fees are shown

Note: American Express ESA transactions will look slightly different. Since American Express deposits the total batch minus the fees, you will need to account for the difference when downloading the transactions. Enter the amount that you were funded into your checking account in the Amount found on Statement field.


Important: The ability to add the AMEX ESA values for the Amount found on Statement field is only available if this feature has been activated. If this option does not appear, please see Activate the 'Amount Found on Statement' field within QuickBooks for AMEX ESA accounts to turn on this ability.

4. Select each deposit or fee you would like to record. You may also click the checkbox in the header to select all deposits or fees.

       Select the deposits and fees to record


5. Click the Record all selected card deposits and fees in QuickBooks button at the bottom of the window.  Once they're downloaded, the deposits and fees will be available for viewing in the QuickBooks bank register.

Manually Record QuickBooks payments Deposits and Fees

In some cases, some or all the information may not download. Once a download attempt fails it cannot be reset and the missing information will need to be manually entered in QuickBooks.


Manually enter a missing deposit(s)

1. In QuickBooks, go to the Banking drop-down and select the Make Deposits option (not make Merchant Service Deposits).

2.  Highlight the appropriate items to be reconciled.

3. Click the Make Deposits button to move the items to the bank account and complete the reconciliation.



Manually enter a missing fee(s)

To enter the missing fee, the corresponding bill will also need to be created.


Create the Bill

1. In QuickBooks, go to the Vendors drop-down and select Enter Bill.

2. At the Enter Bill window, select the vendor assigned for Intuit QuickBooks payments account (if not listed select Add New).

NOTE: Once the vendor is selected, the following information may auto-populate. If so, disregard that related step.

3. Ensure the proper expense account is listed in the Account field.

4. Enter the amount of the fee to be entered in the Amount Due field (that value should also then appear in the amount filed below).

5. Ensure the date is correct for the date of the fee then click the Save & Close button to complete the bill.


Pay the fee.

1. Go back to the Vendors drop-down and select Pay Bills.

2. The bill that was just created will appear here. Place a checkmark next to the bill.

3. If there are multiple bank accounts, be sure to select the bank that the fees were withdrawn.

KB ID# HOW16801
4/24/2017 7:45:55 PM
QYPPRDQBKSWS05 9138 Pro 2017 6b87ca