Ask a Shopify store owner what they pay Shopify and most will quote their monthly plan price. That number is usually the smallest part of the bill. The real cost of running on Shopify is the per-sale payment processing fee, plus a possible surcharge for using an outside payment gateway, plus the app subscriptions that quietly stack up — all of which scale with your store, while the plan fee stays flat.
This guide breaks down every category of Shopify fees, walks through a worked margin example on a single order, and then covers the part most sellers get wrong: how Shopify batches orders into payouts, and why booking the payout deposit as revenue will misstate both your sales and your fees.
The Four Buckets of Shopify Fees
Every dollar you pay Shopify falls into one of four buckets. Two are fixed-ish monthly costs, and two scale directly with sales volume. Knowing which bucket a cost lives in tells you whether growth makes it cheaper per order (fixed costs spread thinner) or simply bigger (variable costs grow with revenue).
- •Subscription plan: the flat monthly fee for your plan tier. Fixed regardless of sales volume.
- •Payment processing: a percentage plus a fixed amount on every transaction. Pure variable cost — this is your 'Shopify fees per sale.'
- •Third-party gateway surcharge: an extra percentage Shopify charges if you process payments through an outside gateway instead of Shopify Payments — on top of whatever that gateway charges you.
- •Apps, themes, and extras: app subscriptions, usage-based app charges, paid themes, domains, and shipping label costs billed through Shopify.
Shopify Plan Tiers and What They Actually Buy
Shopify's core plans run from a basic tier for new stores up through mid and advanced tiers for higher-volume sellers, with Shopify Plus as the enterprise option. Exact prices change periodically, so treat any number you read in an article — including this one — as a snapshot and confirm against Shopify's current pricing page. As a rough frame, the entry plan has historically sat in the tens of dollars per month, the advanced tier in the low hundreds, and Plus at an entirely different negotiated level.
The reason plan tier matters more than the sticker price suggests: higher tiers come with lower payment processing rates. That means there is a crossover point where upgrading your plan pays for itself purely through processing savings. A store doing significant monthly volume on a basic plan is often donating margin — the math on whether to upgrade is just (rate difference) × (monthly card volume) versus the plan price difference.
Shopify Payment Fees Per Sale
If you use Shopify Payments (Shopify's built-in processor), each online card transaction costs a percentage of the order total plus a small fixed amount. US online rates have historically landed in the neighborhood of 2.4%–2.9% plus around 30 cents per transaction, with the percentage falling as your plan tier rises — but these rates vary by plan, country, and card type, so check your plan's current rate card before modeling anything.
If you use a third-party gateway like PayPal, Authorize.net, or Stripe directly, you pay twice: the gateway's own processing fee, plus Shopify's additional transaction surcharge (historically a fraction of a percent to a couple percent depending on plan). This surcharge is why most Shopify stores default to Shopify Payments — running an outside gateway only makes sense when the gateway offers something Shopify Payments can't, like a payment method your customers demand or availability in your country.
One more per-sale wrinkle: when a customer gets a refund, Shopify returns the sale amount but processors generally do not return the original processing fee. High-refund stores effectively pay processing fees on revenue they never keep, which is one reason refund rate belongs on your monthly metrics dashboard right next to conversion rate.
Worked Example: Where a $40 Order Actually Goes
Here is an illustrative breakdown of a single $40 order on a mid-tier plan. Say the product costs $14 landed, shipping runs $6.50, and processing is an illustrative 2.6% + $0.30 — that's $1.34 in payment fees per sale. Now spread the fixed costs: if the plan costs roughly $79/month and you do 200 orders, that's about $0.40 per order; $120/month of app subscriptions adds $0.60 per order.
Total cost on this example order: $22.84, leaving $17.16 of contribution margin — about 43% of the sale. Notice that payment processing alone took 3.4% of revenue (the percentage plus the fixed 30 cents, which stings more on small orders). On a $15 order, that same fee structure takes 4.6%. Fixed per-transaction fees are why low average-order-value stores feel processing costs more acutely than premium stores do.
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How Shopify Payouts Work — and Why a Payout Is Not Revenue
Shopify Payments doesn't send you money order by order. It batches all transactions captured in a period, nets out processing fees and refunds, and deposits one lump sum on your payout schedule. A single bank deposit might contain forty orders, three refunds, and the fees on all of them. The deposit also lags the orders by a few business days, so end-of-month payouts routinely contain sales from one month and land in the next.
This is the single most common Shopify bookkeeping error: booking the bank deposit as sales income. Do that and you understate revenue (fees were already netted out), understate expenses (the fees vanish instead of appearing as a cost), erase refunds from your books, and smear month-end sales into the wrong period. Your gross margin, your sales tax basis, and your month-over-month trend all come out wrong — each by a different amount.
- 1
Customer pays
Card is charged at checkout; Shopify Payments captures the gross order amount.
- 2
Funds enter the payout balance
The transaction joins other captured orders waiting in your pending Shopify balance.
- 3
Fees and refunds are netted
Processing fees, refunds, and adjustments are deducted inside the batch — before anything reaches you.
- 4
Payout is batched
On your payout schedule, Shopify bundles the net amount from many orders into one transfer.
- 5
Deposit hits the bank
One lump sum arrives days after the underlying sales — net of fees, spanning many orders, possibly crossing months.
Booking Shopify Correctly in QuickBooks or Xero
The correct pattern is to record activity gross, then clear the payout against it. For each period, book a summary journal: gross sales as revenue, refunds as contra-revenue, processing fees as an expense, and sales tax collected as a liability — with the net amount sitting in a 'Shopify clearing' account. When the payout lands in the bank, you match it against the clearing account instead of coding it to income. The clearing account should hover near zero; a persistent balance means something — usually a missed refund, a reserve hold, or a fee change — needs investigating.
Doing this by hand from Shopify's payout reports is tedious enough that most sellers either skip it or pay a bookkeeper to grind through it monthly. This is exactly the job tools like BeanHawk automate: it posts summarized settlement journals to QuickBooks Online and Xero so each payout reconciles to the penny, with gross sales, fees, refunds, and tax broken out — flat all-channel pricing from $19/mo if Shopify is one of several channels you sell on.
Apps and Themes: The Fee Bucket Nobody Audits
App charges deserve their own line item review because they grow by accretion. You add a review widget during a launch, an upsell app for a promotion, an email tool you later replace but never cancel. Each looks small alone; together they can rival or exceed your plan fee. Worse, some apps bill on usage — per email sent, per order processed — so they're variable costs wearing a subscription's clothing.
Run a quarterly audit: export your Shopify bill, list every app, and for each one ask what revenue or saved time it can point to. Paid themes are usually a one-time cost and rarely the problem; recurring app charges with no measurable output are. Cancel ruthlessly — unlike processing fees, this is the one Shopify cost category entirely within your control.
A Practical Monthly Checklist for Shopify Fees
Shopify fees aren't a single number — they're a plan fee, a per-sale processing cost, a possible gateway surcharge, and an app stack, each behaving differently as you grow. Once a month, spend twenty minutes confirming the system is healthy rather than discovering problems at tax time.
- •Reconcile every payout: each bank deposit should tie to a Shopify payout report, and your clearing account should net near zero.
- •Check your effective processing rate: total payment fees divided by gross card sales. If it drifts up, look for card-mix changes, more international orders, or a plan-tier mismatch.
- •Re-run the plan upgrade math: (your rate − next tier's rate) × monthly card volume vs. the plan price difference, using current rates from Shopify's pricing page.
- •Audit app subscriptions against actual use; cancel anything that can't justify itself.
- •Verify refunds posted as contra-revenue and that non-returned processing fees on refunds are showing up in your fee expense.
- •If bookkeeping is the bottleneck, automate the settlement journals — BeanHawk or a comparable tool turns this checklist from an afternoon into a five-minute review.