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How to Avoid Duplicate Entries of Merchant Fees in QuickBooks Merchant Account

One of the things that seems to increase my reconciling time is: I get a bunch of duplicate entries for my merchant fees.  Once, when I download my Wells Fargo Bank transactions, and another when I record my credit card deposits in QuickBooks, and it goes the Merchant deposits and fees windows to record the fees again. What is the proper sequence so they match and do not rerecord the same transactions?
Are you going to Banking > Make Merchant Service Deposits before doing your online download?  You need to do this first so that your fees can get matched up to your bank statement.  Try not to enter your fees manually. 

Also keep in mind that if delete the merchant account fees that are downloaded from the merchant center, instead of the fees you entered manually, they’ll just keep downloading every time you Make Merchant Service Deposits.  Do if you have duplicate merchant account fees, make sure to delete the ones that were entered manually from your online banking download. 

The easiest way to tell the difference is that the fees downloaded from the merchant account center have an ID in the memo field on the check.  It'll look something like this:  Fee ID=66335092.  These are the fees you don't want to delete.


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This article is provided for informational purposes and is not intended to be construed as legal, accounting, or other professional advice. For further information, please consult appropriate professional advice from your attorney and certified public accountant.

Ruth Perryman - QuickBooks Specialist Written by +Ruth Perryman

Ruth is the an Intuit Premier Reseller that offers great deals on QuickBooks POS and QuickBooks Enterprise. She has provided expert QuickBooks help to thousands of businesses all over the world since 1996.

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3 Responses to How to Avoid Duplicate Entries of Merchant Fees in QuickBooks Merchant Account

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  • Kathy says:

    My fees for last month are showing up on the pending screen, but they will NOT post. I had to enter them manually to balance, but how do I delete them from the pending screen?

    • Hi Kathy,

      Unfortunately, there’s no way to delete merchant account fees until they’re downloaded. I recommend calling Merchant Services support for help (800-558-9558).