If your customer paid an invoice through SynkedUP Payments and QuickBooks now shows the full invoice amount but your bank deposit is short — that's normal, and the difference is the SynkedUP Payments processing fee. The customer paid in full; the fee just doesn't live on the invoice. This article explains what's happening and the exact steps to record the fee in QuickBooks so everything balances.

Say your customer was billed $5,467.13 and paid the whole thing via credit card. Here's what shows up:

That $218.99 is the SynkedUP Payments processing fee. It's deducted from your payout (the money that lands in your bank account), not added to the invoice (what your customer pays). So the customer paid in full, the invoice is recorded in full, and the fee comes out of your side.

This is the same way every credit card processor works — Stripe, Square, PayPal, etc. The fee doesn't appear as a line item on the invoice; it's withheld from the deposit.

For the fee rates by transaction type, see SynkedUP Payments Fees.

The cleanest way is to record the fee on the bank deposit side in QuickBooks — not as a change to the invoice. This keeps the invoice tied to what your customer actually paid, and puts the fee in the right expense account for your books.

Using the $5,467.13 / $218.99 / $5,248.14 example:

Result: the invoice stays at $5,467.13 (correct — that's what the customer paid), the bank deposit shows $5,248.14 (correct — that's what landed), and the $218.99 fee is recorded as a business expense (correct — it's a cost of accepting card payments).

If you don't already have a Credit Card Fees expense account in your chart of accounts, create one — it's a standard merchant-fee expense and most accountants will expect to see it there at year-end.

If you're not sure what fee was withheld on a specific transaction, check SynkedUP:

The net payout figure should match the deposit amount in your bank — that's the number you reconcile against.

Right. The customer paid the full invoice. The deposit in your bank account is short by exactly the processing fee — that's a cost of accepting card payments, not a shortfall from the customer.

Same idea — same workflow. ACH has a different fee rate (1.00% capped at $1,000 vs. card's 3.50% with no cap), but the mechanics are identical: the fee is withheld from the payout, and you record it the same way in QuickBooks. For the rate comparison see SynkedUP Payments Fees.

Yes — each invoice gets its own payout, so you'll add one negative fee line to each deposit in your bank register. The good news: the fee math is the same every time (the gross payment minus the fee equals the deposit), so once you've done a couple, it's a quick habit.

Yes — we're working on an in-product flow to help with recording these fees automatically. We'll update this article when it ships.

If the deposit, invoice, and fee numbers don't add up cleanly — for example, the fee shown in Settings → Payments → Payouts doesn't match the gap between the invoice and your bank deposit — send us a message in the chat box with the invoice number and the payout date, and we'll take a look.