If you sell on Shopify, the fee on each order is small enough to ignore per sale and big enough to quietly eat your margin over a month. This guide shows you the exact formula, the current rates, and a full per-order profit example — then explains why the number you calculate here still won't equal the deposit in your bank.
The Shopify fee-per-order formula
Every Shopify Payments order carries two parts: a percentage of the order value and a flat fee. The formula is simple:
Per-order fee = (order total × card rate) + fixed fee
The order total here is what the customer actually pays — subtotal plus shipping plus tax — because the card is charged the full amount. The card rate depends on your plan. The fixed fee is a flat charge on every transaction, no matter how small the order.
That flat fee is why small orders hurt most. On a $5 order, 30¢ is 6% before you even count the percentage rate. On a $200 order, that same 30¢ is a rounding error.
Shopify Payments rates by plan
The percentage side of the fee drops as you move up plans. These are the current US online rates for Shopify Payments, per TrueProfit's 2026 fee breakdown:
| Plan | Online card rate | Fixed fee |
|---|---|---|
| Basic | 2.9% | 30¢ |
| Grow | 2.7% | 30¢ |
| Advanced | 2.5% | 30¢ |
| Plus | Negotiated volume rate | 30¢ |
Two things to note. First, "in-person" (POS) rates are lower than the online rates above — this article covers online orders. Second, these rates apply only when you use Shopify Payments. If you route payments through a third-party gateway like PayPal, Shopify adds its own transaction fee — around 2.0% on Basic, 1.0% on Grow, and 0.6% on Advanced — on top of the gateway's charges.
Worked example: the fee on one $49 order
Say you sell a print-on-demand mug. The customer pays $40 for the product, $5 shipping, and $4 tax, for a $49 order total. You're on the Basic plan.
Run the formula:
Per-order fee = ($49 × 2.9%) + $0.30 Per-order fee = $1.421 + $0.30 Per-order fee = $1.72
So Shopify keeps $1.72 of that $49 charge as processing. That's the number most fee calculators stop at — but it tells you almost nothing about whether the order made money.
From fee to per-order profit
The processing fee is one line in a longer stack. To know what you actually earned, subtract everything that order cost you. Keep going with the same $49 order:
- Order total collected: $49.00
- Less sales tax you remit (not yours): −$4.00
- Less product cost from your POD supplier: −$12.00
- Less the shipping you pay to fulfill it: −$5.00
- Less the Shopify processing fee: −$1.72
- Less ad spend to win the customer: −$10.00
Per-order profit = $49.00 − $4.00 − $12.00 − $5.00 − $1.72 − $10.00 = $16.28
The Shopify fee was $1.72 — real, but the smallest variable in the stack. Product cost, fulfillment, and ad spend moved your margin far more. This is the angle most "Shopify fee calculator" pages skip: the fee alone never tells you if an order was profitable. You have to reconcile it against every other cost on the same order.
Doing that by hand for one order is easy. Doing it across hundreds of orders — each with its own product cost, supplier invoice, and ad-attributed spend — is where merchants lose the thread. If you want the mechanics of matching supplier bills and payouts back to individual orders, our guide to reconciling your ecommerce data walks the full process.
The extra fees that hit some orders
The base formula covers most domestic sales. Several add-ons apply only in specific cases, and each one changes the per-order math:
- Currency conversion. When a customer pays in a currency different from your payout currency, Shopify adds a conversion fee — 1.5% for US stores, up to 2.0% for international stores — on top of the normal rate.
- International cards. Cards issued outside your store's country cost more; TrueProfit puts the blended charge near 3.9% plus 30¢ per transaction.
- Chargebacks. A disputed order costs you the refund plus a dispute fee of roughly $15 per chargeback in the US, and Shopify debits it straight from your payout.
- Shopify Tax. Once your US sales pass a threshold, Shopify charges 0.35% on orders where tax is calculated, capped per order and per year.
None of these show up on every order, so a flat "fees are 3–5% of revenue" rule of thumb hides the variance. A store selling mostly to overseas buyers pays a very different effective rate than one selling domestically.
Why your payout never matches your calculated fees
Here's the part that trips up nearly every first-time reconciler: the fee you calculate per order does not line up cleanly with your bank deposit. A Shopify payout is a batch of balance transactions settled together, not one day's orders minus fees.
A payout equals captured charges, minus processing fees, minus any refunds issued in that period, minus chargeback debits, plus or minus reserve adjustments. Refunds and disputes from earlier orders land in today's payout, and orders paid through PayPal or other outside gateways never enter a Shopify Payments payout at all.
So "gross sales minus fees equals my deposit" is the classic reconciliation error. If you've ever stared at a deposit that's smaller than expected, our breakdown of why Printify charges before your Shopify payout clears and why a Printful invoice doesn't match your order count show the same timing gap from the supplier side.
Getting true per-order profit without a spreadsheet
Calculating one order's fee is a formula. Calculating true profit on every order — fee, product cost, fulfillment, and the ad spend that actually drove each sale — is a data problem, because those numbers live in five different systems that each count differently.
That's what PodVector is built for. It connects Shopify, Meta Ads, Google Ads, Printify, and Printful, then computes your true per-order profit — the $16.28 in the example above — across all of them, so the processing fee, supplier cost, and attributed ad spend land on the same order.
On top of that live data sits Victor, an AI operator who analyzes your numbers and proposes moves, then executes the ones you approve on the Shopify side. Victor reads your ad data to explain which orders actually made money, but he does not touch your ad account — the writes he makes are Shopify-side, with your sign-off. If ad attribution is where your numbers fall apart, the guide to the best app for Google Ads pixel tracking on Shopify covers the tracking layer that feeds this math.
FAQs
How do I calculate the Shopify fee on a single order?
Multiply the order total (subtotal plus shipping plus tax) by your plan's card rate, then add the fixed per-transaction fee. On Basic that's the order total times 2.9%, plus 30¢, per TrueProfit's rate breakdown. A $49 order works out to about $1.72.
Is the Shopify fee charged on the subtotal or the full total?
On the full total the customer pays. The card is charged for product, shipping, and tax together, so the percentage rate applies to that whole amount — not just the product subtotal.
Why is my Shopify payout less than my total sales minus fees?
Because a payout is a batch of balance transactions, not a day's orders minus fees. It also subtracts refunds and chargebacks from earlier orders and excludes anything paid through third-party gateways. Reconcile it against balance transactions, not against your sales report — the ecommerce data reconciliation guide explains why.
Do lower Shopify plans always cost more per order?
On processing, yes — Basic's 2.9% rate is higher than Advanced's 2.5%, according to TrueProfit. But higher plans cost more in monthly subscription, so the break-even depends on your order volume. Run your monthly order count through the fee formula on each plan before switching.
Does the Shopify fee include my product and shipping costs?
No. The Shopify fee is only the payment-processing charge. Product cost, fulfillment shipping, and ad spend are separate — and as the worked example shows, they usually dwarf the processing fee when you calculate true per-order profit.
How much of my revenue do Shopify fees typically take?
Field estimates put total Shopify fees near 3–5% of revenue depending on plan and payment mix, but that blends processing, currency, and other charges — Webgility's payout breakdown details the components. The effective rate is higher for stores with lots of international or disputed orders.