Hidden Marketplace Fees: What Cuts Your Payout in Australia

The fees that hurt Australian marketplace sellers most are rarely the headline commission. They are the smaller, conditional charges that sit inside a payout: fees calculated on shipping as well as the item, refund administration fees, currency conversion charges, advertising and label deductions, and dispute costs. Each looks minor on one order, but across thousands of orders and several channels they can move margin by whole percentage points, and they are easy to miss because marketplaces deduct them before the money reaches you.

The headline fees everyone knows

Every marketplace advertises its main charges. Amazon Australia's Professional plan costs $49.95 a month excluding GST, and most referral fees fall between 6% and 15% depending on category (Amazon Australia, 2026). eBay Australia lets Australian-registered sellers without a Pro plan and with AU$25,000 or less in sales over the past 12 months sell without transaction fees, though they generally need to use eBay's shipping labels (eBay Australia, 2026).

These numbers are useful for a first pass. They are not what you will actually pay per order.

Seven charges that hide inside payouts

1. Commission on shipping, not just the item. Amazon AU calculates its referral fee on the total sales price, which includes delivery and gift wrap charges, with no minimum or maximum (Amazon Seller Central, 2026). If you charge $15 shipping on a 13% category, roughly $1.95 of fee sits on the freight line alone.

2. Tiered and split rates. Several Amazon AU categories change rate at a price point. Clothing, for example, is listed at 10% for items $20 or less and 13% above $20, while Jewellery is charged at 15% up to $200 and 5% on the portion above. A small price change can move a product into a different band.

3. Refund administration fees. When you refund an Amazon AU order after being paid, Amazon returns the referral fee minus a refund administration fee of the lesser of $5.00 or 20% of the referral fee (Amazon Seller Central, 2026). A refunded sale is therefore never fully cost-neutral.

4. Per-item closing fees. Amazon AU adds a $1.00 closing fee per media item sold, such as books, music and video games, on top of the referral fee.

5. Currency conversion. eBay states that from 1 November 2026, the seller currency conversion charge rises to 3.25% when eBay converts funds for an item listed or sold on another eBay site (eBay Australia, 2026). Shopify Payments also charges multi-currency payout fees when you choose a non-domestic default payout currency (Shopify, 2026).

6. Deductions that are not "fees" at all. eBay lists ad fees, shipping labels, monthly subscriptions, Money Back Guarantee refunds and payment dispute refunds among the costs automatically deducted from your sales proceeds (eBay Australia, 2026). If proceeds do not cover them, eBay charges your card or bank account instead, which means some costs never appear in the payout at all.

7. Disputes and chargebacks. On your own storefront, a card dispute costs more than the refunded amount. Mastercard reports that each chargeback costs merchants an average of $128 in third-party fees and internal costs (Mastercard, 2025). We cover tracking these in how to track refunds and chargebacks across channels.

GST adds another layer

Marketplaces do not all present fees the same way. Amazon AU states its fee schedule prices are in Australian dollars and do not include GST, while eBay says fees on its Pro pages are now displayed inclusive of Australian GST (eBay Australia, 2026). If your reconciliation treats both the same way, either your fee cost or your GST credits will be wrong. This is general information only; see the ATO's GST guidance and your adviser.

How to find the fees you are actually paying

• Calculate an effective fee rate per channel. Divide all marketplace deductions (fees, ads, labels, refund fees, currency charges) by gross sales for the same period. Compare that to the advertised commission.
• Build expected-fee rules. For each marketplace and category, write down the rule: rate, base (item only or item plus shipping), thresholds and fixed charges. Then compare each order's actual fee to the expected one.
• Separate fee types in your ledger. Post commission, advertising, fulfilment, labels and refund-related fees to different accounts so trends are visible.
• Watch the change logs. Marketplaces update fee pages regularly. eBay's own page lists several changes due in November 2026 alone.
• Review returns cost by channel. Refund admin fees, return shipping and non-resaleable stock belong in channel profit, as discussed in our guide to profitability per sales channel.

Key figures

• Most Amazon AU referral fees are between 6% and 15%, plus $49.95 a month excluding GST for the Professional plan (Amazon Australia, 2026).
• Amazon AU keeps a refund administration fee of the lesser of $5.00 or 20% of the referral fee when an order is refunded (Amazon Seller Central, 2026).
• eBay's seller currency conversion charge increases to 3.25% from 1 November 2026 (eBay Australia, 2026).
• Chargebacks cost merchants an average of $128 each in fees and internal costs (Mastercard, 2025).

How eComChannels helps

eComChannels Finance auto reconciliation lets you set fee rules per marketplace and category, including the base the fee is calculated on, price thresholds and fixed charges. When each settlement arrives, it compares the fees actually deducted against the expected amount for every order and lists the exceptions, so overcharges and miscategorised products surface within days rather than at year end. Refunds are linked back to the original sale held in eComChannels order management, so refund administration fees and returned commission are visible per order.

Because all channels sit in one view, you can see your true effective fee rate for Amazon, eBay, Kogan, BIG W Market and your own store side by side, and price or allocate stock with real numbers. That reduces finance hours spent checking payouts by hand and recovers money that would otherwise go unclaimed. Book a demo or start a 30-day free trial.

FAQ

Are marketplace fees calculated on the shipping I charge?

On some marketplaces, yes. Amazon AU calculates referral fees on the total sales price, including delivery. Check each marketplace's fee page, because the base differs between platforms.

Do I get my commission back when I refund a customer?

Usually only in part. Amazon AU returns the referral fee less a refund administration fee. Other marketplaces have their own rules, so track refunded fees order by order.

How do I know if a marketplace overcharged me?

Compare the fee on each order with the fee the published rules say should apply. Doing this by hand is slow, which is why most sellers only find errors when they automate the check.