Margin-Leak Audit

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Payment fees on Shopify: how to find what you actually paid

Payment fees are a cost on every order, and unlike product cost they are easy to leave out of a margin calculation because they never appear on a product page. This guide does not quote rates, because they vary by plan and country and change over time. It shows how to find your own numbers and how to use them.

What Shopify says about how fees work

Per Shopify's Help Center, with Shopify Payments you pay a credit card rate and no separate transaction fee. With a third-party payment provider, there is a Shopify transaction fee plus the provider's own card fees. Your credit card rate depends on your Shopify plan. Your standard rates are shown in your admin under Settings > Payments > Shopify Payments > Manage, and a specific payout shows an overview of the fees you were charged for that payout.

The Help Center page does not describe the export columns or whether fees are listed per transaction, so check your own payout and transaction exports to see what detail you get. If you use a third-party provider, your fee detail will come from that provider's statements as well.

Turn fees into a number you can use

  1. Choose a period, say the last 90 days, and take the total of sales for the period from Shopify.
  2. Take the total of fees for the same period, from your payout details or your provider's statements. Include any Shopify transaction fee if you use a third-party provider.
  3. Divide fees by sales. This is your effective fee rate. It will usually differ from the headline rate, because of refunds, order mix, currency and other factors.
  4. Use this rate, not the headline rate, in any margin calculation. The discount impact calculator has fields for a percentage and a fixed fee per order; enter your own.

The result is yours alone. Do not use a rate from a blog post, including this one.

Where fees interact with other leaks

Refunds. Shopify's Help Center says credit card fees are not returned on refunds with Shopify Payments, and transaction fees are also not refunded with a third-party gateway where Shopify Payments is available. A refunded order can therefore still cost you the original fee. See returns.

Discounts and shipping. Fees are charged on what the customer pays, so they fall when discounts reduce the price, but a fixed per-order component does not. Small, heavily discounted orders carry the highest fee burden relative to what they earn. See discount codes.

Currency and international orders. If you sell in other currencies, check whether your statements show a conversion cost. The Help Center page we reviewed does not cover this, so look at your own payout and bank records rather than assuming.

What to look for

Limits of this guide

Fee structures vary, and the official pages we relied on describe where to look, not what you will find. If a number on your statement surprises you, ask your payment provider or accountant.

Prefer someone to read the statements with you?

The Margin-Leak Audit reads fees order by order against your sales when you supply payout data, and states its assumption where you do not. Or start with the Margin Leak Self-Check.

Sources

Help Center pages change. Check the current page before relying on a detail.

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