Shopify fees explained: what Shopify really takes from a $100 sale
The subscription is the fee people notice. The processing fee on every order is the one that quietly adds up.
On a standard $100 online sale with Shopify Payments on the Basic plan, Shopify takes 2.9% plus 30 cents, which is $3.20. On top of that per sale fee you pay a monthly subscription, from $39 on Basic, and an extra percentage if you use a third party payment gateway instead of Shopify Payments. The processing fee is charged on every order, so it scales with sales.
How much does Shopify take from a $100 sale?
On the Basic plan with Shopify Payments, a $100 online card sale costs 2.9% plus 30 cents in processing, which is $3.20, leaving $96.80 deposited to you. That is just the transaction fee. It does not include your monthly subscription, which is separate, or the cost of the product itself. Higher Shopify plans charge a slightly lower processing percentage.
The $3.20 is deducted before Shopify pays you, so it never shows as a line item in your bank; it is simply missing from the deposit. That is what makes processing fees easy to overlook. They are not billed to you, they are withheld from what you are owed, which is why so many stores book gross sales and quietly overstate their profit by the fee.
What are the different Shopify fees?
There are four you are likely to meet: the monthly subscription for your plan, the payment processing fee on each sale, an extra third party transaction fee if you use a gateway other than Shopify Payments, and chargeback fees when a customer disputes a payment. Currency conversion adds a further small fee on international sales.
| Fee | When it applies | Rough cost |
|---|---|---|
| Subscription | Monthly, for your plan | From $39/mo on Basic |
| Payment processing | Every card sale via Shopify Payments | 2.9% + 30¢ online (Basic) |
| Third party gateway fee | If you use an external payment provider | Up to 2% extra on Basic |
| Chargeback | When a customer disputes a payment | A fixed fee per dispute |
| Currency conversion | Sales in a currency other than your payout | A small percentage per order |
Why did Shopify charge me $39?
A $39 charge is almost always your Basic plan subscription, billed monthly. It is separate from the per sale processing fees and is charged whether or not you made any sales that month. If you were charged $39 unexpectedly, it is the recurring Basic plan fee coming due, not a fee tied to a particular order.
Shopify's plans step up from there, and each higher tier trades a bigger monthly fee for a lower processing percentage and more features. The maths of whether a higher plan pays off comes down to volume: the plan fee is fixed, so the more you sell, the more the lower processing rate saves you.
How do I avoid Shopify transaction fees?
You cannot avoid the payment processing fee, since every card sale carries one somewhere. But you can avoid Shopify's extra third party transaction fee by using Shopify Payments as your processor rather than an outside gateway. On Basic that extra fee can be up to 2% per order, so switching to Shopify Payments removes it entirely.
The other lever is your plan. Because higher plans lower the processing percentage, a store doing enough volume can pay less in total by upgrading, even after the larger subscription. Beyond that, the fees are a cost of accepting cards, and the useful move is not avoiding them but accounting for them accurately so your profit numbers are honest.
How to see your true Shopify fees per order
Shopify's payout reports show fees per payout, but not cleanly per order, and they do not fold in refunds, chargebacks or currency losses into a single profit figure. To see the real fee on each order you either build it from exported payout data, or use a tool that reads every order's actual fees and subtracts them from revenue automatically.
Margio breaks down the real Shopify fee on every order, transaction fees, currency conversion, chargebacks and refunds, and subtracts them to show true profit per order rather than an estimate. Because it works from the actual fee on each sale, a refunded or internationally converted order is costed correctly instead of at a flat assumed rate.
On the Pro plan, Margio also confirms those fee deductions against your real bank deposits, so the fee figure is verified by the money you actually received, not just what Shopify reported.
Frequently asked
Why are Shopify fees so high?
Most of the cost is the card processing fee, 2.9% plus 30 cents per online sale on Basic, which is close to the industry standard for card payments rather than a Shopify markup. Fees feel high because they are charged on every order and withheld before payout, so they accumulate quietly rather than arriving as one visible bill.
Is it cheaper to sell on Etsy or Shopify?
It depends on volume. Etsy charges a listing fee plus a transaction and payment fee per sale but no monthly platform cost, which suits low volume sellers. Shopify charges a monthly subscription plus processing, which becomes cheaper per sale once you are selling enough to spread the fixed fee. High volume favours Shopify; occasional selling favours Etsy.
Does Shopify charge a fee if I don't use Shopify Payments?
Yes. If you use a third party payment gateway instead of Shopify Payments, Shopify adds an extra transaction fee on top of whatever your gateway charges, up to 2% per order on Basic and lower on higher plans. Using Shopify Payments removes that extra fee.