Here's a quick summary of the differences between how you'll see Stripe's Fees within QuickBooks Online:
Merchant Fees is what you'll see added to the Invoice for when a client pays Stripe's Fees on their side.
Payment Processing Fees is what you'll see being taken out of the Deposit for all of Stripe's Fees.
I'm passing Stripe's Fees
I have a Project in Goodshuffle Pro for $102.50 ($100 line item + $2.50 tax).
The client paid the entire contract total and paid Stripe's Fees for a total of $106.14.
On the Invoice in QuickBooks Online I'll see Line Items for $100.00 and $2.50 in Tax and a Merchant Fee - Payment Processing Fee Line for $3.64.
This will make the total $106.14 so QBO can match the Payment from the client (including the Fees).
The Payment will be for the total amount paid (including any fees paid by the client). You'll also see a note on the Payment outlining any Fees included in the transaction.
This Payment will be matched to the corresponding Invoice automatically.
When the Deposit is transferred to my bank account, I'll see $106.14 in the total payments, and Line at the bottom for Merchant Fees (Paid by Client) for $3.64.
The total sent to my bank will be $102.50
When viewing this from the Merchant Fees account in QuickBooks Online, I will see these balancing transactions:
I'm accepting Stripe's Fees on my side:
On the Invoice I'll see Line Items for 100.00 (with no Merchant Fee Line).
When the Deposit is transferred to my bank account, I'll see 100.00 in the total payments, and Line at the bottom for Merchant Fee for 1.00.
The total sent to my bank will be 99.00
It's important to note that these Merchant Fees are purely to track the total dollar amount that you charged the client and should not be confused with the Payment Processing Fees related to Bank Deposits that reflect the net processing fees for all of the charges and refunds grouped within that particular Bank Deposit.
Be sure you’re in the know when it comes to all merchant services fees by reviewing this (Article).