How to record Square, Shopify, PayPal and Afterpay payouts (fees and GST)

Record each payout in parts: the sales, less any refunds, less the fees, all through a clearing account for that platform. Then record the payout itself as a transfer from that clearing account to your bank. Do that and the deposit matches your bank statement to the cent, and your GST comes out right.

Here's why, how to do it by hand, and the report to download from each platform.

Why don't my payouts match my sales?Link to this section

Shopify, Square, PayPal and Afterpay don't pay you sale by sale. They collect your customers' money, take out their fees and any refunds, and pay you the rest in one lump.

So a $1,012 deposit might really be $1,100 of sales, a $55 refund and $33 of fees:

Your bank

1. Sales$1,100$100 GST included
2. Refunds−$55Takes $5 off the GST on sales
3. Fees−$33$3 GST to claim, if the tax invoice shows it
4. Deposit in your bank$1,012A transfer, not a sale

• Sales $1,100, including $100 GST.
• Less refunds $55, including $5 GST.
• Less fees $33, including $3 GST you can claim if the platform's tax invoice shows it.
• Equals the deposit in your bank, $1,012, recorded as a transfer.

If you record the $1,012 as sales:

• Your sales are too low, so your BAS (the form you send the tax office each quarter) and your profit and loss are wrong
• The fees disappear, so you lose an expense
• You miss the GST (the 10% tax on most things you sell) you can claim back on fees that include it

Is there GST on Square, Shopify, PayPal and Afterpay fees?Link to this section

It depends on the platform, so check each one rather than assuming.

• Square says it charges GST on its processing fees and puts a monthly tax invoice in your Square Dashboard on the 5th of the next month, if you took card payments. See Square's tax reporting and GST invoices FAQ (opens in a new tab).
• Shopify Payments says GST at 10% is included in all its processing fees in Australia, with a monthly invoice generated on the 5th of the next month. See Shopify's tax reporting for Australia (opens in a new tab) page. Your Shopify plan and app charges come on a separate bill.
• PayPal and Afterpay: look at what their statements and fee documents say about GST before you claim any. If there's no GST shown, there's nothing to claim.

To claim GST on a fee you need the platform's tax invoice, so download those monthly invoices and keep them with your records. Not sure how a fee is treated? Ask your accountant or BAS agent. This is general information, not tax advice.

What's a clearing account?Link to this section

A clearing account is a bank-style account in your books for money a platform is holding for you. Think of it as your "Square balance" or "Shopify balance".

• Sales go in
• Refunds and fees come out
• Each payout moves what's left to your real bank account

If everything's recorded, it comes back to about zero after each payout. If it doesn't, something's missing. That makes it a handy check, which is why bookkeepers love them.

How do I record a payout by hand?Link to this section

Say a payout of $1,012 hits your bank. The platform's report shows $1,100 of sales (GST included), one $55 refund and $33 of fees. In your books:

Check: $1,100 less $55 less $33 is $1,012. The clearing account is back to zero, and the bank line matches the transfer when you reconcile.

Doing this for one payout is fine. Doing it for a payout every day, on two or three platforms, is where the afternoons go.

What about payouts that cross the end of a month?Link to this section

A Friday's sales might be paid out on Monday, which can be next month or next quarter. The sales belong to when your customer paid, not when the money reached your bank. So date the sales, refunds and fees on the days they happened, and only the transfer on the payout date. Your clearing account holds the money in between, and each BAS gets the right figures.

How do I handle refunds, disputes and held money?Link to this section

• Refunds reduce your sales and the GST on them. Record them as refunds, not as expenses.
• Disputes (chargebacks) work like a refund: the money taken back reduces your sales. Any dispute fee is a fee. If you win, the money coming back counts as a sale again.
• Money held back. If a platform holds some of your money for a while, it's still yours. Move it to a held funds account on your balance sheet, and back when it's released. Your profit and GST don't change.

Which report do I download from each platform?Link to this section

Each platform has a report that lists every sale, refund and fee, and which payout it went into. These are the ones Billbook reads, named the way the platforms name them. Menus change, so search for the report's name in the platform or its help pages.

• Shopify Payments: the payout transactions export. Add the orders export if you sell things without GST, so each order's real GST comes through.
• Square: the transactions export, with the Deposit ID and Deposit Date columns.
• PayPal: the activity download, choosing balance-affecting transactions.
• Afterpay: the settlement export from the Afterpay Business Hub.
• Stripe: the itemised payout reconciliation report.

Start each export a few days before the first payout you want, so every payout is whole. Our help page on which file to download from each platform has the detail.

Two gaps to watch. PayPal or Afterpay used at your Shopify checkout are paid out by PayPal or Afterpay, not in Shopify's payouts, so they need their own file. And cash taken through Square never reaches a deposit, so record it when you bank it.

How does Billbook record payouts?Link to this section

You download the file and add it in Billbook. It does the four steps above for every payout in the file:

Payout, 14 OctMatched

Sales$1,100.00$1,100.00

Refunds−$55.00$55.00

Fees (GST $3.00)−$33.00$33.00

To your bank$1,012.00$1,012.00

• Sales go in as one invoice per payout, to a customer named after the platform, paid into that platform's clearing account
• Refunds and disputes go in as a credit note
• Fees go in as spend money, with the GST the platform charges on them
• The payout becomes a transfer to your bank, so the deposit matches in one go

When a payout crosses the end of a month, each month's sales and fees are dated in that month. Files can overlap, because Billbook remembers every line it brings in and leaves out repeats. If a platform renames its columns, Billbook works out the layout with AI and shows you the payouts it found before anything goes in. Everything lands as ordinary invoices, credit notes and spend money, so you can change any of it after.

It's free on every plan. You import the files yourself, so nothing needs access to your store.

The step by step is in import payouts and how payouts go into your books. There's more on the apps and payouts features page.

What are the common mistakes?Link to this section

• Coding the deposit as sales. It's the most common one, and it gets worse each quarter.
• Counting sales twice. If you've already coded deposits as sales in your bank, don't import the same dates on top. Undo the coding first.
• Claiming GST on fees without a tax invoice. Keep the platform's monthly invoice.
• Leaving out the platform's own bill. Shopify's monthly bill for your plan and apps isn't in your payouts. Add it as a bill.
• Forgetting the clearing account check. If it doesn't come back to about zero, something is missing. Usually a payout outside the dates of your export.

When is the BAS due?Link to this section

Import your payouts at least before each BAS, so the quarter's sales and fees are in.

1. Q1Jul to SeptDue 28 October 2026
2. Q2Oct to DecDue 28 February 2027
3. Q3Jan to MarDue 28 April 2027
4. Q4Apr to JunDue 28 July 2027

Our BAS due dates tool shows the next one, and our guide to lodging your BAS yourself covers the rest.