Author: Duncan Warnock CPA | April, 2022 

How to allocate a QuickBooks Merchant Payment 

There are alternate ways to manage the bookkeeping of a Merchant facility payment for a Customer invoice  in QuickBooks. This article provides a simple & accurate way that will ensure the correct customer payment amount is recorded and the correct merchant fee expense is recorded. The example scenario is for a business that is GST registered and charge GST to their customers and also claim back GST on expenses incurred where the supplier has charged GST.

Scenario Summary 

  1. Customer Heath Row has been issued Invoice 1002 that totals $300 including GST 
  2. Customer Heath Row paid the full invoice amount of $300 via a merchant facility 
  3. The Merchant charged $30 in merchant fees for the transaction
  4. The Merchant paid the business owner $270 after deducting $30 from the $300 transaction 

Objective - Allocate the $270 received money transaction that accurately records a $300 customer payment (including GST)  to the customer invoice and records the $30 (including GST)  business merchant fee business expense  $300 customer payment 


  1. Log into QuickBooks
  2. Navigate to the Banking menu and then select FOR REVIEW to view the unallocated transactions 
  3. Select the unallocated RECEIVED MONEY transaction you wish to allocate and click on it to open the full display of the transaction 
  4. Select the FIND MATCH radio button to search for the unpaid invoice(s) you wish to allocate the payment to 
  5. Select the Invoice(s) you wish to allocate the Received Money transaction to 
  6. Adjust the AMOUNT of the RECEIVED MONEY transaction being allocated to the Customer Invoice (in this example amend $270 to $300) 
  7. The amount being allocated ($300) now does not match the actual money received into the Bank Account ($270) 
  8. Select the 'Resolve Difference' option 
  9. Add details of the Merchant Fee expense ( -$30 in this example) and also record Date, Payee & record a description 
  10. CHECK that the Payment being allocated ($270) matches the amounts being allocated ($300 less $30 = $270) 
  11. Click SAVE to complete the payment allocation

For further information or assistance contact Duncan Warnock CPA at Warnock Accounting today. 

Contact us via phone 0402 210 614 or alternately email duncan@warnockaccounting.com.au. Warnock Accounting looks after clients from all over Geelong, the Bellarine and the Surf Coast. 

Alternately submit your contact details via our website contact us form via this website. 



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