Why Your Shopify Payout Never Matches Your Sales

You sold $10,000 last week. $8,400 landed in your bank. Nothing is wrong, but almost nobody explains where the rest went — and if you don't know, you can't reconcile your accounts or trust your own numbers.

Here's the full path from a sale to a bank deposit.

Why is my payout smaller than my sales?

Four things happen between the two, and they compound.

1. Transaction fees come out first

Shopify Payments deducts its fee before paying you. The rate depends on your plan and country, typically around 2%–3% plus a fixed amount per transaction. International cards usually carry a surcharge.

Buy-now-pay-later is the one that surprises people. Afterpay, Klarna and similar often charge 4–6% — materially more than card processing. If BNPL is a big share of your orders, your blended fee rate is higher than you think.

2. Refunds are deducted from the payout, not the original sale

Refund an order from three weeks ago and it comes out of this week's payout. So a payout can be reduced by sales that were never part of that period — which is exactly why payout totals never tie neatly to a date range of orders.

3. Chargebacks and reserves

Disputed transactions are held or deducted. Some stores — newer ones, higher-risk categories, or those with a sudden volume spike — have a rolling reserve, where Shopify holds a percentage for a period.

4. The timing is offset

Shopify pays out on a delay that varies by country and plan. So the money arriving today relates to orders from several days ago. A payout period and a sales period are never the same window, and comparing them directly will always produce a discrepancy.

Worked example

A week's trading:

Swipe to see more →

Every deduction is legitimate. But if you're recording $10,000 as revenue and $8,798 as the deposit without reconciling, your books won't balance and you won't know why.

What about the GST inside all this?

This is where it gets genuinely confusing, and it's worth being careful.

Your $10,000 of sales, if GST-registered in New Zealand, includes roughly $1,304 of GST that isn't yours. Your Shopify fees also generally have GST in them, which you can claim back.

So the $8,798 that landed contains:

• Your actual revenue
• GST you're holding for IRD
• Net of fees you can partly reclaim GST on

Which is exactly why treating your bank balance as profit goes wrong so reliably. See how much to set aside for GST and tax.

How do I reconcile payouts properly?

Use the payout report, not the sales report. Shopify's Finances → Payouts section breaks down each payout into gross sales, refunds, fees and adjustments. That breakdown is what reconciles to your bank, not the orders list.

Reconcile payout-by-payout, not by date range. Trying to match a calendar month of sales to a calendar month of deposits will never work because of the timing offset. Match each individual payout to its bank line.

Record the components separately. Sales, fees and refunds are three different things in your accounts. Booking the net deposit as revenue understates both your income and your expenses — and your accountant will either fix it or charge you to fix it.

Watch your blended fee rate. Add up fees across a month and divide by gross sales. If it's drifting up, it usually means BNPL or international orders are becoming a bigger share — useful to know, because it directly affects margin.

What this means for knowing your profit

Even perfectly reconciled, a payout still isn't profit. It's revenue minus Shopify's fees, offset in time. It doesn't know about:

• what you paid your supplier
• what you spent on ads
• what the courier charged
• the GST you're holding

So the payout answers "what did Shopify send me," which is a cash question. It does not answer "did I make money," which is the one that matters.

Closing that gap is precisely what we built Rev Room for — it takes Shopify orders, deducts real product costs, actual per-order shipping from Starshipit or GoSweetSpot, and ad spend from Meta, Google and TikTok, then shows profit with GST and tax set-asides separated out for NZ and Australian stores.

You can absolutely do the same reconciliation manually. The important thing is knowing that the payout and the profit are different questions.

The short answer

• Payouts are net of fees, refunds and chargebacks, and offset in time
• Refunds hit the payout they're processed in, not the one the sale was in
• BNPL fees are roughly double card fees — check your blended rate
• Reconcile payout-by-payout against the payout report, never sales-by-month
• A payout is a cash number; profit is a different question entirely

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Related reading: Revenue vs profit · How much to set aside for GST and tax · Do you need a business bank account?

General information only, current as at 20 August 2026. Fee rates vary by plan, country and payment method — check your own Shopify settings. Talk to your accountant about how to record payouts.