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Shopify hidden fees explained

Shopify's headline pricing is only part of the story. The fees that actually decide whether a product is profitable are the per-order ones — and they are easy to underestimate. Here is where your margin really goes.

Payment processing fees

With Shopify Payments you typically pay 2.9% + $0.30 per online transaction on the Basic plan, with lower percentages on higher plans. That fixed $0.30 matters more than it looks: on a $5 item it is 6% on its own.

Third-party gateway surcharge

If you use a payment gateway other than Shopify Payments, Shopify adds a transaction fee on top — often around 2%. Stacking that on your processor's own fees can quietly double your per-order cost.

App subscriptions

Every paid app is a fixed monthly cost that has to be spread across your orders. A handful of $15-$30 apps adds up to real overhead per order at low volume.

Chargebacks and disputes

A single chargeback can cost you the product, the shipping and a dispute fee — far more than the order was worth. A few a month is a real leak.

Currency conversion

Selling in a currency other than your payout currency can incur a conversion fee on every order — small per order, meaningful across thousands.

Shipping gaps

Not a fee exactly, but the same effect: when the shipping you pay exceeds what you charge, the difference is a cost on every order.

A worked example

Take a $30 order: about $1.17 in processing (2.9% + $0.30), maybe $0.60 for a third-party gateway, plus a share of app costs and any shipping gap. Before product cost, you may already be down 6-10% — which is why a "healthy" gross margin can still end in a thin or negative net.

Run your own numbers with the Shopify fee calculator and the profit margin calculator.