QuickBooks Online Credit Card Fee Reconciliation
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Here’s how credit card fees will be recorded in QuickBooks Online if you are absorbing them for your customers.
We’ve made it easier to reconcile any credit card fees that are absorbed back to your QuickBooks Online integration so you can ensure all your accounts receivables are up up to date.
NOTE: The fee reconciliation workflow applies only if deposit creation is enabled in Alternative Payments. If it is not enabled, fees must be reconciled manually.
These fees will now be recorded automatically as funds in the deposits within QuickBooks Online and will show as “Alternative Payments Fees” for each transaction with a negative dollar balance to account for the fee absorbed for each transaction.

Alternative Payments will create the payment in QuickBooks Online for the full invoice amount.
A negative balance for the fees will be added to the deposit in QuickBooks Online that states “Alternative Payment Fees” for the fees that were absorbed.
For your payout, we will deposit the payment and add the negative balance so the deposit amount matches your bank balance.
Example (Please see the above image)
The payment for the full amount is created in QuickBooks Online for $100
A -$1 is automatically added to the deposit
The fee will go to an account called “Alternative Payments Fees” within QuickBooks Online
This fund will relate to the same customer that the invoice is associated with
The $99 amount listed is the same amount as your payout from Alternative payments.
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