If your Shopify dashboard says you sold $10,000 last week but only $9,200 landed in your bank, nothing is broken. That gap is normal and predictable, and once you know what it’s made of, you can reconcile it in a few minutes per payout instead of untangling a year’s worth at tax time.
The trouble starts when you skip that step. Recording the deposit as your sales figure feels harmless, but it understates what your store actually turned over and throws off the tax you report. Here’s where the money goes between the sale and the bank, and how to keep your books straight without hiring anyone before you need to.
What sits between a sale and the deposit
Every platform payout is a net number. The customer pays the full price at checkout, then the platform and the payment gateway take their cut before the rest reaches you. Four things account for almost all of the difference.
- Processing fees. Shopify Payments, Stripe and PayPal each keep a percentage of every transaction plus a fixed few cents. Depending on the card and the country, that’s typically somewhere between 1.7% and 2.9% per order. On thin margins, that alone is the whole gap.
- Refunds and partial refunds. If you refund an order inside a payout window, the platform nets it out of that deposit. Your gross sales for the period were still real, but the cash that arrives is lower.
- Chargebacks and disputes. A disputed charge gets pulled back, often with a dispute fee on top, and it may reverse weeks after the original sale sat in an earlier payout.
- Rolling reserves. Some gateways, especially on newer or higher-risk accounts, hold back a percentage of your revenue for a set period (commonly around 90 days) before releasing it. That money is yours, but it isn’t in the deposit yet.
Marketplace payouts behave the same way with extra layers. An Amazon or eBay settlement bundles referral fees, fulfilment charges, ad spend and returns into one figure, so the deposit can be a long way from what the storefront rang up. The mechanism is identical: gross sales at the top, deductions in the middle, net cash at the bottom.
Timing makes it worse. A single Shopify deposit rarely maps to a single day’s orders. It bundles a rolling window of transactions minus any refunds processed in that window, so you can’t just match one deposit to one day’s sales and call it done.
Why booking the deposit as revenue quietly breaks your numbers
Say your store did $10,000 in gross sales, paid $280 in processing fees, and refunded one $200 order. The deposit is roughly $9,520. If you enter $9,520 as revenue, two things go wrong at once.
Your turnover looks smaller than it was. That skews your reported margins and growth, and any financing or valuation conversation that leans on revenue. You also lose the expense line entirely, because the $280 in fees never gets recorded as a cost you can claim.
The second problem is tax. In Australia, GST is calculated on the gross sale, not on what’s left after the gateway takes its fee. Book the net deposit as revenue and you understate the sales you made and the GST you collected on them. That’s how a Business Activity Statement drifts out of line, and the error repeats every quarter until someone catches it.
A reconciliation workflow you can repeat
The fix is a routine you run against each payout instead of a once-a-year clean-up.
- Pull the gross sales for the payout period from the platform, not the bank. In Shopify that’s the Finances summary or the payouts report, which shows gross, fees and refunds separately. 2. Record gross sales as revenue and fees as an expense. Don’t collapse them into one net line. Your bookkeeping software should show the full sale and the processing cost side by side. 3. Match the net payout to the bank deposit. If Shopify says the payout was $9,520 and your bank shows $9,520, that leg reconciles. If it doesn’t, a refund or reserve is usually the reason. 4. Track refunds, chargebacks and reserves as their own entries so you can see money that’s been held back rather than lost. 5. Repeat per channel. Shopify, Stripe, PayPal, Amazon and eBay each get their own reconciliation, because each reports and deducts differently.
Apps like A2X or Link My Books automate most of this by turning each payout into a summarised journal that already splits sales, fees and refunds before it reaches your accounting software. They’re worth it once payouts get frequent. A tidy spreadsheet does the same job while you’re small and running a single channel.
When to bring in an accountant
Reconciliation stays manageable while one storefront pays you on a steady schedule and your only deduction is the processing fee. It stops being manageable when there is more to track: several gateways each with their own reserve rules, and marketplace settlements that fold advertising and returns into one figure while GST still has to be right on every gross sale rather than the net that shows up in the bank.
A Shopify, Stripe or PayPal payout lands in your account net of processing fees, refunded orders, chargebacks and, on some gateways, a rolling reserve the platform holds back, so the deposit is always smaller than the gross sales figure your dashboard reports. Book that deposit as your revenue and you understate both your turnover and the GST you actually collected, which is exactly how Business Activity Statement errors creep in and compound quarter after quarter. Firms that work only with online retailers, such as Brisbane-based Walker Hill, reconcile each platform payout back to gross sales before anything reaches the BAS, so the numbers you lodge match what the store really earned. Once you are reconciling payouts from more than one channel and collecting GST across state lines, a spreadsheet stops keeping up, and this is usually the point where Australian sellers bring in specialist ecommerce accounting help rather than guess at what each bank deposit actually represents.
FAQ
Is the deposit ever the same as my sales? Only if you had zero fees, refunds and reserves in that window, which essentially never happens once you’re taking card payments. Treat a matching deposit as a coincidence, not a rule.
Should I record revenue when the sale happens or when the payout lands? Record revenue at the point of sale, at the gross amount. The payout is a cash movement that follows later, and matching it to the bank is a separate reconciliation step.
Do I owe GST on the fees the gateway keeps? GST applies to the gross sale you made to the customer. The processing fee is your own business expense, which may carry its own GST you can claim, so keep the two separate rather than netting them off.
What’s the earliest sign my books are drifting? Your recorded revenue is consistently lower than the sales the platform reports. If those two numbers don’t line up each month, the deposit is being booked as revenue somewhere.
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