Key takeaways
What this article covers, in order:
- The problem with "Shopify deposit: $3,255.60"
- Clearing accounts: the idea that fixes all of this
- Worked example 1: a Shopify-style payout
- Worked example 2: an Amazon-style settlement
- Etsy: lots of small fees
- What about stock?
The short answer for ecommerce bookkeeping: never record a marketplace payout as one lump of "sales". A payout is gross sales minus fees, refunds and sometimes advertising, so you record each piece separately and run them through a clearing account for each platform. Do that, and your bank reconciliation lines up and your profit figure is actually true.
The problem with "Shopify deposit: $3,255.60"
Josh makes soy candles in Ballarat and sells through his own Shopify store, an Etsy shop and, since mid-2026, Amazon. Every few days a deposit lands in his account with a platform name on it.
For his first year he coded every deposit to "Sales". It felt fine. Then his accountant asked why his sales figure was lower than the total in his Shopify dashboard, and why there were no platform fees anywhere in his expenses.
Both questions have the same answer. The deposit is a net figure. The platform has already taken its fees and paid out refunds before the money reached him. If you code the net amount as sales:
- your sales are understated,
- your fees are invisible, so you can't see what each channel really costs,
- refunds disappear, and
- your GST coding is very likely wrong, because sales and fees are treated differently.
Clearing accounts: the idea that fixes all of this
A clearing account is a temporary holding account on your balance sheet. Set one up for each platform: "Shopify clearing", "Etsy clearing", "Amazon clearing".
The flow looks like this:
- Record the gross sales into the clearing account (it goes up).
- Record fees and refunds out of the clearing account (it goes down).
- Record the payout from the clearing account to your bank (it goes down again).
When everything's right, the clearing account goes back to zero, or to whatever the platform is still holding for you. If it doesn't, something's missing, and you've found it before your accountant did.
Worked example 1: a Shopify-style payout
Josh's weekly payout report for the week ending 18 Oct 2026 shows:
| Line | Amount |
|---|---|
| Gross sales | $3,480.00 |
| Refunds | −$120.00 |
| Payment processing fees | −$104.40 |
| Net payout to bank | $3,255.60 |
Check: $3,480.00 − $120.00 − $104.40 = $3,255.60.
In his books, that becomes:
- Sales: $3,480.00 (into Shopify clearing)
- Refunds: $120.00 (out of Shopify clearing, recorded against sales or a refunds account)
- Merchant fees expense: $104.40 (out of Shopify clearing)
- Transfer to bank: $3,255.60 (out of Shopify clearing)
Clearing balance afterwards: $3,480.00 − $120.00 − $104.40 − $3,255.60 = $0.00. When the bank feed shows the $3,255.60 deposit, you match it to that transfer, not to "Sales".
Worked example 2: an Amazon-style settlement
Marketplace settlements usually have more lines. Here's Josh's settlement for a period ending 15 Oct 2026:
| Line | Amount |
|---|---|
| Product sales | $5,200.00 |
| Referral (selling) fees | −$780.00 |
| Fulfilment fees | −$612.50 |
| Advertising | −$240.00 |
| Refunds | −$95.00 |
| Net settlement to bank | $3,472.50 |
Check: $5,200.00 − $780.00 − $612.50 − $240.00 − $95.00 = $3,472.50.
Same pattern: record sales gross, each fee to its own expense account, refunds against sales, and the settlement as a transfer to the bank. Keep the settlement report (download it from your seller account) as the source document. It's the evidence for every number.
Two quirks worth knowing:
- Settlement periods don't line up with calendar months. A settlement that runs from 24 Sep 2026 to 8 Oct 2026 needs to be split by date if you want accurate monthly figures, or at least handled consistently. Pick a rule with your accountant and stick to it.
- Sometimes the platform holds money back (a reserve) or a settlement comes out negative. That's exactly why the clearing account exists: it shows what the platform still owes you, or what you owe it.
Etsy: lots of small fees
Etsy shops tend to have many small charges: listing fees, transaction fees, payment processing, advertising, and sometimes postage labels bought through the platform. You don't need a separate account for each one. A sensible split for most small sellers:
- Marketplace fees (listing, transaction, processing)
- Advertising
- Postage and shipping
Use the monthly statement from your shop dashboard, total each type, and record them in one entry per month against Etsy clearing. Then match the payouts as transfers.
What about stock?
If you hold stock, the cost of the candles you sold is a separate question from the payout. For small sellers on a cash approach, stock purchases often just get coded as cost of goods when bought. Once you're holding meaningful inventory, you'll want to track stock on hand and value it at year-end. That's a conversation for your accountant, and a reason to look at inventory tracking once you've outgrown a spreadsheet.
A monthly checklist for online sellers
- [ ] Download the payout or settlement report for every platform
- [ ] Record gross sales, refunds and each fee type per platform
- [ ] Match each bank deposit to its payout as a transfer from clearing
- [ ] Check each clearing account balance makes sense (zero, or a known amount held)
- [ ] Record any platform charges taken from your card instead of the payout (ads billed separately, subscription apps)
- [ ] Reconcile the bank account itself
- [ ] Save the payout reports with the month's records
GST, briefly
Sales and platform fees often carry different GST treatments, and overseas platforms add their own wrinkles. Code each line as correctly as you can, keep the reports, and let your BAS agent or accountant handle lodgement. If you sell across borders or through several marketplaces, it's worth a one-off session with them to set up your coding properly at the start.
Common mistakes we see
- Coding net deposits as sales. Covered above. It's the big one.
- Ignoring app subscriptions. Store apps and themes billed to your card are real expenses and add up.
- Treating refunds as an expense. Refunds reduce sales. Most owners want to see sales after refunds, so either record them against sales or in a refunds account that sits under income.
- Mixing platforms in one clearing account. When something doesn't balance, you won't know which platform caused it.
- Waiting until the end of the financial year. Twelve months of settlement reports is a horrible weekend. Do it monthly.
How HelloBooks helps
In HelloBooks you connect your bank account (most Australian banks and cards are supported) or import a CSV statement. Each deposit lands in a review list where you confirm or change the category, so a payout can be treated as a transfer from clearing instead of being dumped into sales.
The reconcile screen lines up your bank statement against your ledger with an AI match suggestion on each line, showing a confidence score and why it picked that match. You only work through the exceptions, and when the month's done you get a reconciliation report (opening balance, cleared items, outstanding items, closing balance) as a PDF or CSV.
On Pro (A$30 a month), AI auto-categorisation and unlimited bank connections help when you're running several accounts and cards, and multi-currency with auto FX is there if a platform pays you in another currency. Advanced inventory sits on the Business plan. Read more about automated bookkeeping or see pricing.
FAQs
Should I record sales gross or net of platform fees?
Gross. Record the full sale, then record fees as an expense. Net recording hides your costs and makes your sales look smaller than they are.
What is a clearing account in e-commerce bookkeeping?
It's a temporary balance-sheet account for each platform. Sales go in, fees, refunds and payouts come out, and the balance should end at zero or at whatever the platform is still holding.
How do I handle a payout that covers two months?
Either split it by the dates on the settlement report or apply one consistent rule all year. Agree the approach with your accountant so your year-end figures aren't distorted.
Do I need a separate bank account for my online store?
It helps a lot. If your store payouts land in the same account as your personal spending, sorting them out each month takes far longer.
What if a settlement is negative?
Record it the same way. The clearing account will show you owe the platform, and the next settlement (or a card charge) settles it.
Get one platform's clearing account balancing this month and the others will follow the same pattern.
Start free, no card needed. Try HelloBooks Free
