Key takeaways
What this article covers, in order:
- Why the deposit never equals your sales
- The clearing account method
- Each processor has its own quirks
- Payouts that cross a month-end
- A weekly payout routine
- When the numbers won't line up
A payout from a payment processor is rarely one sale. It's usually a bundle: several days of sales, minus fees, minus any refunds or chargebacks, sometimes held back or released on a schedule. To reconcile it, you record the gross sales and the fees separately and use a clearing account so the net deposit that hits your bank matches exactly. Square reconciliation works this way, and so do Stripe, Tyro and PayPal: the processor's payout report is the document that ties the two together.
Why the deposit never equals your sales
Lucas runs a coffee cart at weekend markets around Adelaide and takes cards through a payment terminal. On Monday 7 Sep 2026 his bank shows a deposit of $1,904.80. His sales for the weekend were $2,000.00. Where did $95.20 go?
His processor's payout report tells the story:
| Item | Amount |
|---|---|
| Card sales, Sat 5 Sep 2026 | $1,180.00 |
| Card sales, Sun 6 Sep 2026 | $820.00 |
| Gross sales | $2,000.00 |
| Refund to a customer (wrong order) | minus $60.00 |
| Processing fees | minus $35.20 |
| Net payout to bank | $1,904.80 |
Check: $1,180.00 + $820.00 = $2,000.00. Then $2,000.00 minus $60.00 minus $35.20 = $1,904.80. The $95.20 gap is the refund plus the fees.
If Lucas codes the $1,904.80 deposit straight to Sales, three things go wrong. Sales are understated by $95.20, his fees disappear from his expenses (so he can't see what card payments cost him), and the GST on sales is calculated on the wrong figure.
The clearing account method
The fix most bookkeepers use is a clearing account, sometimes named after the processor ("Square clearing", "Stripe clearing"). Think of it as a holding bay that sits between your sales and your bank.
- Record gross sales into the clearing account. $2,000.00 of sales, coded to Sales with the right GST code, goes into clearing. Clearing balance: $2,000.00.
- Record the refund out of the clearing account. $60.00 against Sales. Clearing balance: $1,940.00.
- Record the fees out of the clearing account. $35.20 to Merchant fees. Clearing balance: $1,904.80.
- Match the bank deposit to the clearing account. The $1,904.80 arriving in the bank is a transfer from clearing to the bank. Clearing balance: $0.00.
When the clearing account is back to zero, everything has been accounted for. If it's not zero, something is missing: a payout not yet received, a fee not recorded, or a refund that slipped through.
Each processor has its own quirks
The method is the same for all of them, but each one behaves a bit differently. Settings change and vary by account, so always confirm against your own statements and payout reports rather than assuming.
Square
Payouts typically bundle a day's or several days' card sales, with fees taken out before the money reaches you. Square's reports separate gross sales, refunds and fees, which is exactly what you need for the clearing method. If you also take cash through the same point-of-sale, keep cash sales separate; they don't go through the payout.
Stripe
Common for online businesses and subscriptions. Payouts usually arrive net of fees on a rolling schedule, and one payout can include charges from several days, refunds and dispute adjustments. Stripe's payout reconciliation report lists every transaction inside a payout, which makes it easy to build one summary entry per payout.
Tyro
Popular with cafés, retailers and health practices using in-store terminals. Depending on your merchant agreement, settlement may arrive as gross sales with fees charged separately (for example as a monthly debit), or net of fees. Check your Tyro statement to see which applies to you. If fees come out as a separate monthly line, code that line to Merchant fees and record your daily settlements at their full amount.
PayPal
PayPal behaves more like a separate account than a pass-through. Money can sit in your PayPal balance for a while, be used to pay suppliers directly, or be converted between currencies before you withdraw it. Many bookkeepers treat PayPal as its own account in the books, record sales, fees and purchases there, and then record withdrawals to the bank as transfers. If you sell overseas, watch currency conversion; any FX difference needs recording.
Payouts that cross a month-end
Sales on 30 Sep 2026 might not be paid out until 2 Oct 2026. If you only record sales when the money arrives, sales for Sep 2026 look low and sales for Oct 2026 look high.
With the clearing method, sales for Sep 2026 are recorded in Sep 2026, which leaves a balance in the clearing account at 30 Sep 2026. That balance is the payout still on its way. On 2 Oct 2026 the deposit clears it. Your Sep 2026 reports are right, and your bank still reconciles to the statement because the deposit genuinely arrived in Oct 2026.
A weekly payout routine
- [ ] Download each processor's payout report for the week
- [ ] Post one summary entry per payout: gross sales, refunds, fees, any chargebacks
- [ ] Match each bank deposit to its payout in the clearing account
- [ ] Check every clearing account balance; anything left should be a payout you're still waiting on
- [ ] Look up any balance that has sat in clearing for more than a week
- [ ] Make sure the GST codes on sales and fees are right; your BAS agent or accountant handles lodgement
One summary entry per payout is usually plenty. You don't need every individual coffee in your books; your point-of-sale or processor keeps that detail.
When the numbers won't line up
A few usual suspects:
- Reserves or holds. Some processors hold back part of a payout for a period. That money is still yours, so it stays in the clearing account until it's released.
- Chargebacks. These can be taken out of a later payout. Record them against the original sale, plus any fee.
- Fees charged elsewhere. Monthly terminal rental or subscription fees may come straight from your bank account rather than out of payouts.
- Two processors, one bank account. Make sure each deposit is matched against the right processor's clearing account.
If you're stuck on a large or recurring gap, ask your bookkeeper to look at a full month of payout reports alongside the bank.
How HelloBooks helps
In HelloBooks you work from the bank side. Processor payouts arrive through your connected bank account (we support most Australian banks and cards) or a CSV statement import, and land in a review list where you confirm or change the category. At month-end the reconcile screen lines your statement up against your ledger with an AI match suggestion on each line, showing a confidence score and why it picked that match, so you only work through the exceptions. The reconciliation report (opening balance, cleared items, outstanding items, closing balance) exports as PDF or CSV for your accountant. Your processor's payout report remains the source for the gross sales and fee figures. See our bank reconciliation software and cash flow management pages.
FAQs
Should I record card sales gross or net of fees?
Gross. Record full sales and record the fees separately as an expense. Recording net hides your fees and understates your sales.
What is a clearing account for payment processors?
A holding account between your sales and your bank. Sales go in, refunds and fees come out, and the payout to the bank empties it. A zero balance means everything is accounted for.
How do I handle PayPal fees?
Record the sale at its full amount and the PayPal fee as a separate expense. If PayPal is set up as its own account in your books, both sit there until you withdraw to the bank.
Why is my Tyro deposit the full sale amount with no fee taken?
Some merchant agreements settle gross and charge fees separately, often monthly. Check your statement for a separate fee line and code it to merchant fees.
Do I need to record every single card transaction?
Usually not. One summary entry per payout, backed by the processor's report, is enough for most small businesses.
Gross sales in, fees out, deposit matched, clearing at zero. Do that weekly and processor payouts stop being a mystery.
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