Most Australian Shopify merchants set up Shopify Payments once during store setup and rarely think about it again, until the amount landing in their bank account doesn’t match what they expected, or a bookkeeper asks why gross sales in Shopify don’t reconcile with bank deposits. Both of those situations come down to the same thing: understanding what Shopify Payments actually charges, when it pays out, and what the deposited figure represents.
This isn’t a pricing announcement, exact transaction rates depend on your Shopify plan and change from time to time, so we’re not going to guess at numbers that might be wrong by the time you read this. Instead, this post explains the mechanics: how the fee structure is built, how payout timing generally works, and how to reconcile what Shopify reports against what actually hits your bank account. For your current exact rates, check Settings > Payments in your Shopify admin, which always reflects what you’re actually being charged.
How Shopify Payments fees are structured
Shopify Payments charges a transaction fee on each order processed through it, and that fee is generally built around a few consistent principles across Shopify’s plans, even though the exact percentages differ by plan tier and change periodically:
- Fees vary by plan tier. Higher Shopify plans (and Shopify Plus) generally come with lower Shopify Payments transaction rates than entry-level plans, as part of the value of paying more for the platform itself. The exact current rate for your plan is shown in Settings > Payments > Manage in your admin.
- Card-present and card-not-present rates differ. Transactions taken online (card-not-present) typically carry a different rate to transactions taken in person through Shopify POS with a physical card tap or insert (card-present), reflecting the different fraud risk profile between the two.
- An additional fee applies if you don’t use Shopify Payments as your payment gateway. If you use a third-party payment gateway instead of Shopify Payments, Shopify charges an extra transaction fee on top of whatever your third-party processor charges. This is one of the main reasons most Australian merchants stick with Shopify Payments rather than an external gateway, it avoids paying two sets of fees.
- International cards may attract an additional fee. Cards issued outside Australia can incur an extra percentage on top of the standard rate, which is worth knowing if you sell internationally or run ads targeting overseas customers.
- Currency conversion, if enabled, is a separate cost. If you sell in multiple currencies through Shopify Payments’ multi-currency feature, conversion fees apply separately from the standard transaction fee.
Because these figures are reviewed and occasionally adjusted by Shopify, don’t rely on a number you read in a blog post, including this one, always confirm your current rate in Shopify admin before quoting it to your accountant or building it into pricing calculations.
How Shopify Payments payout timing works
Once a customer pays, that money doesn’t land in your bank account instantly, it goes through a payout cycle. In general terms, Shopify Payments follows a standard payout schedule (commonly the next business day for many merchants, though this can also be set to a different cadence such as every few days depending on your account), subject to a few conditions:
- New accounts often have a slightly longer initial payout delay. This is standard practice for most payment processors, not specific to Shopify, it gives the platform time to build a transaction history and manage fraud risk before releasing funds on the fastest possible schedule.
- Weekends and public holidays affect “business day” timing. A payout scheduled for a Saturday will typically land the next business day instead, which is worth factoring into cash flow planning around long weekends.
- Risk review can hold or delay payouts. Shopify, like any payment processor, applies fraud and risk monitoring, and unusual activity, a sudden spike in order volume, a large single transaction, or a pattern that looks like fraud, can trigger a manual review that delays payout until it’s cleared.
- Reserves can apply in higher-risk categories. Some industries or account risk profiles may have a rolling reserve (a portion of funds held back for a period) rather than the full amount paying out immediately. This is more common for certain product categories or newer accounts with limited trading history than for established, low-risk stores.
You can see your actual payout schedule and any pending or held amounts under Settings > Payments > Payouts in Shopify admin. This is the authoritative source for your specific account, general payout timing described here is a starting expectation, not a guarantee for every merchant.
Why your bank deposit doesn’t match your gross sales
This is the point that trips up a lot of merchants and their bookkeepers. The amount that lands in your bank account is not your gross sales figure, it’s gross sales minus a few deductions, and reconciling the two requires looking at the right report.
The deposited amount typically differs from gross sales because of:
- Transaction fees, deducted before payout rather than billed separately
- Refunds processed since the last payout, which reduce the net amount
- Chargebacks or disputes, which can be deducted and may include an additional dispute fee
- Shopify subscription and app charges, if you have your Shopify bill set to draw from your payment balance rather than a separate card
- Any reserve or hold amount, if applicable to your account
For example, imagine a week where a store processes $10,000 in gross sales, has $300 in refunds, and pays roughly 2% in transaction fees on the net processed amount. The actual bank deposit for that period will be noticeably below $10,000 once fees and refunds are accounted for, and if your bookkeeper is only looking at the “gross sales” figure in Shopify reports without factoring in the payout report, the numbers will never tie out.
How to reconcile Shopify payouts against your bank statement
- Pull your payout report, not your sales report, as the starting point. In Shopify admin, go to Settings > Payments > Payouts (or Finances > Payouts, depending on your admin layout) to see each individual payout, its date, and its breakdown of gross amount, fees, refunds, and adjustments.
- Match each payout to a corresponding bank deposit by date and amount. Most merchants find it easiest to reconcile weekly or monthly rather than trying to match every individual payout in real time.
- Check the fee breakdown within each payout, not just the net total, so you understand what proportion of the gap is fees versus refunds versus other adjustments.
- Reconcile GST separately from the payout figure. The GST component of your sales sits within your gross sales, not as a separate line Shopify Payments deducts, so your accounting system needs to calculate GST from the sales data itself, not try to derive it from what lands in the bank.
- Flag any unexplained variance. If a payout amount doesn’t match what your fee calculation and refund records predict, check for holds, reserves, or a disputed transaction before assuming it’s a bookkeeping error.
- Keep payout reports for your accounting file, since your accountant will generally want the payout-level detail rather than just a bank statement total when preparing BAS or annual accounts.
A practical checklist for staying on top of Shopify Payments
- Confirm your current transaction fee rate in Settings > Payments rather than relying on a remembered figure
- Review your payout schedule and understand whether you’re on daily, or a different cadence
- Check whether any reserve applies to your account, particularly if you’re newer or in a higher-risk category
- Reconcile payout reports against bank deposits on a set schedule, not ad hoc
- Make sure your bookkeeper or accounting software is using payout-level data, not gross sales, to reconcile bank deposits
- Review refund and chargeback activity monthly, since both affect payout timing and amount
- Re-check your rate after any Shopify plan change, since moving plan tiers can change your transaction fee
When this is worth getting outside help
Reconciling Shopify Payments against your accounting system is manageable for a low-volume store doing it manually. It gets genuinely difficult once you’re processing a meaningful volume of daily transactions, running multiple sales channels, or trying to keep Xero, MYOB, or another accounting platform automatically in sync with Shopify’s payout data rather than re-entering figures by hand.
This is where a proper Shopify ERP integration earns its keep, connecting your Shopify payout and order data directly to your accounting or ERP system so reconciliation happens automatically rather than through manual report-matching every week. If you’re still doing this by hand and it’s taking hours each month, it’s usually a sign the integration work would pay for itself quickly.
FAQ
Are Shopify Payments fees the same on every Shopify plan?
No. Transaction fees generally scale with your plan tier, with higher plans typically carrying lower rates as part of the overall value of that plan. Always check Settings > Payments in your own admin for your exact current rate rather than assuming it matches another store’s.
Why did my payout come in lower than expected?
The most common reasons are transaction fees, refunds processed since your last payout, and occasionally a chargeback or dispute deduction. Check the detailed breakdown within your payout report in Shopify admin rather than comparing gross sales directly to your bank deposit.
How long does it take for Shopify Payments to pay out after a sale?
Payout timing generally follows a standard schedule set on your account, commonly around the next business day for many merchants, though this varies and can be affected by weekends, public holidays, and any risk review Shopify applies. Check Settings > Payments > Payouts for your account’s actual current schedule.
Do I need to charge GST separately, or does Shopify handle it?
Shopify Payments processes the payment amount you charge, including GST, but doesn’t calculate or remit GST on your behalf, that’s a tax obligation you manage through your accounting setup. If you haven’t configured GST correctly in Shopify, it’s worth checking our guide on Shopify GST setup to make sure your product pricing and tax settings are correct.
Why does my accountant say Shopify sales figures don’t match my bank account?
This almost always comes down to comparing the wrong report, gross sales in Shopify’s sales reports don’t reflect fees, refunds, or timing differences between when an order is placed and when it’s actually paid out. Reconciling from the payout report, not the sales report, resolves this in nearly every case.
Get your reconciliation process sorted
If matching Shopify payouts to your bank account and accounting system is eating up hours every month, it’s worth looking at whether an automated integration would solve it properly. Book a call with our team to talk through your current setup, or start with a Shopify audit to see where the gaps are.
