Card fees: on the invoice, or on the deposit?

Every card payment costs you a fee. The customer paid 264.54; the processor kept 7.97; 256.57 reached your bank inside a payout. The fee has to land somewhere in QuickBooks. There are two clean places for it, and mixing them is how deposits stop matching.

Option 1: take the fee off each invoice

Add the fee as a minus line on the invoice itself, posting to your merchant fees expense account.

The invoice, and the payment against it, equal the money you actually received: 256.57.
The payout’s deposit is simply the sum of its payments (less any refunds).
Your sales still show the full 264.54 on the product and shipping lines; the fee line brings the invoice total down.

Good when you like each invoice to say exactly what arrived, or your bookkeeper reconciles order by order.

Option 2: leave invoices at the order total, fees on the deposit

The invoice and payment stay at 264.54. When the payout arrives, the deposit gathers the payments and adds one minus line per sale (or one for the whole payout) for the fees, posting to merchant fees.

Invoices match the customer’s receipt exactly.
The deposit still equals the bank line, because the fee lines bring it down.

Good when customers or sales reports need the invoice to equal what was charged, and you’d rather see fees together on each deposit.

The one rule: pick one and keep to it

Trouble starts when some fees are on invoices and others on deposits, or when a fee is recorded twice (once on the invoice, again on the deposit). The deposit then comes out short or long by exactly the fees, and nobody can say why. Write the choice down, and if you change it, change it from a clear date.

Refunds and fees

Processors usually keep the original fee when you refund, and some charge a little more. Either way the change shows up in the payout, so record it on that payout’s deposit as a fee line rather than adjusting the old invoice.

In NemoWorks Sync

It’s one switch: Settings, Payments, Card fees on the invoice. On, each invoice gets a minus line for the processor’s fee. Off, each sale’s fee goes on its payout’s deposit instead. Either way the deposit equals the bank line, and a deposit that can’t is stopped with the reason (how payouts are booked).