If you are comparing gateways at the consideration stage, you have probably noticed every provider quotes a slightly different percentage-and-fee combo. This guide breaks down the three pricing models, shows what the major gateways charge with sources, and walks a per-order calculation so you can see the fee land on your margin — not just on a pricing page.
The three payment gateway pricing models
Every gateway's price fits one of three structures. Knowing which one you are being sold matters more than the specific rate.
Flat-rate pricing
Flat-rate charges the same blended percentage on every card, regardless of what the card network actually costs the processor. Square and Stripe both run this model, with Stripe at 2.9% + 30¢ online and Square at 2.6% + 10¢ in person, according to CoreCommerce's 2026 pricing breakdown. It is predictable and simple to reconcile. The trade-off: the flat rate overcharges you on cheap debit cards to subsidize expensive rewards cards, and gives you no visibility into the underlying cost.
Interchange-plus pricing
Interchange-plus splits the bill in two: the actual interchange fee the card network sets, plus a fixed markup from your processor. The same CoreCommerce breakdown puts consumer credit interchange at roughly 1.4%–1.9%, debit near a few cents over a tiny percentage, and typical small-merchant markups at 0.20%–0.50% plus 10–20¢. Because you pay real network cost plus a transparent margin, it usually beats flat-rate once you are past a few thousand dollars a month — that same source pegs the crossover around $3,000–$5,000 in monthly volume.
Subscription (membership) pricing
Subscription pricing swaps a big percentage markup for a fixed monthly fee plus interchange pass-through and a small per-transaction cost. As the NMI payments pricing guide explains, this model suits higher-volume merchants where a blended flat rate becomes expensive. For a small store doing modest volume, the monthly fee often outweighs the savings — it is a scale play, not a starter plan.
What the major gateways actually charge
Here are current published US rates for standard online card payments. Rates fall as you move to higher plan tiers, so always confirm against the provider's own page for your plan.
| Gateway | Standard online rate | Source |
|---|---|---|
| Stripe | 2.9% + 30¢ | stripe.com/pricing |
| Shopify Payments | ~2.9% + 30¢ (lower tiers) | A2X Shopify fees guide |
| PayPal Checkout | 3.49% + 49¢ | PayPal business fees |
| PayPal Advanced Card | 2.89% + 29¢ | PayPal business fees |
Two details the pricing pages bury. First, if you run Shopify but use an external gateway instead of Shopify Payments, Shopify adds its own transaction fee on top of whatever the processor charges — the A2X Shopify fees guide covers how this stacks. Second, PayPal Checkout's 3.49% + 49¢ is meaningfully higher than the flat-rate crowd, though its Advanced Card rate is competitive.
Worked example: what the fee costs per order
Sticker rates hide inside your margin. Walk a single order to see it.
Say your store sells a product for $40, with a supplier cost of $16. On a 2.9% + 30¢ gateway, the processing fee on that order is:
$40 × 0.029 = $1.16, plus $0.30 = $1.46 per order.
That is 3.65% of the order once you add the fixed fee — higher than the headline 2.9%, because the 30¢ weighs more on a small ticket. Your gross profit before other costs is:
$40 − $16 product − $1.46 processing = $22.54 per order.
Now scale it. Run 250 orders in a month at that $40 ticket and the gateway takes:
250 × $1.46 = $365 in fees on $10,000 of sales.
Switch that same volume to a 3.49% + 49¢ gateway and each order costs $40 × 0.0349 + $0.49 = $1.88, or 250 × $1.88 = $470 — a $105 monthly difference on identical sales, purely from pricing model. On tighter tickets the gap widens, because that fixed per-transaction fee is a bigger slice of a smaller order.
The lesson: the fixed cents matter as much as the percentage. A low-average-order store gets punished by the flat fee; a high-ticket store barely notices it. Match the pricing model to your basket size, not to the biggest number on the ad.
The fees that never make the pricing page
Two costs sit outside the headline rate and quietly eat profit.
Refunds keep the fee. When you refund a customer, the original processing fee is generally not returned to you. So a refunded $40 order still costs you that $1.46 — you kept none of the sale and still paid to process it. Track refunds as contra-revenue and leave the fee where it landed. Our deeper breakdown of payment gateway charges walks through how to book these correctly.
Disputes carry a flat penalty. A chargeback on Shopify Payments costs $15 in the US, refunded only if you win the dispute, according to the A2X Shopify fees guide. A handful of disputes can erase the margin on dozens of clean orders.
These are exactly the line items that make a gateway's effective rate higher than its advertised rate. When you compare pricing, compare the all-in cost per order, not the percentage on the homepage.
From gateway fee to true profit
A pricing model only matters relative to your whole profit picture. The processing fee is one line in your cost of goods sold, sitting alongside product cost and shipping — and beneath it, ad spend usually dwarfs everything. Our ecommerce P&L guide shows where each fee belongs on the statement, and why a high gross margin can still hide a losing store once acquisition cost is counted.
The catch is that these costs live in different systems. Your gateway fee is in Stripe, your product cost is in Printify or Printful, your ad spend is in Meta and Google, and your orders are in Shopify. Reconciling them by hand — the way this article's per-order math does — is slow and easy to get wrong. If you want to see this automated, Shopify accounting apps is the next step, and it helps to first be clear on what a P&L actually is.
PodVector connects your Shopify, Meta Ads, Google Ads, Printify, and Printful accounts and computes true per-order profit — the gateway fee, the product cost, and the ad spend all landed on the same order. Victor, its AI operator, reads that live data and proposes moves you approve, executing the writes on the Shopify side. It is not a dashboard you have to read; it is an operator that does the reconciliation for you. Start free and see your real per-order margin.
FAQs
What is the average payment gateway pricing rate?
Standard flat-rate plans cluster around 2.9% + 30¢ for online card payments in the US, which is Stripe's published rate. But your effective rate is almost always higher, because the fixed per-transaction fee weighs more heavily on small orders and refunds don't return the fee. Calculate your all-in cost per order rather than trusting the headline percentage.
Is interchange-plus cheaper than flat-rate pricing?
Usually, once you are past a few thousand dollars in monthly volume. The CoreCommerce breakdown puts the crossover around $3,000–$5,000 per month, because interchange-plus passes through the real (often lower) network cost instead of a blended rate that overcharges on debit. Below that volume, flat-rate's simplicity often wins.
Do I pay the gateway fee when I refund a customer?
Generally yes. The processing fee on the original sale is usually not returned when you issue a refund, so a refunded order costs you the fee even though you kept none of the revenue. Our payment gateway charges article explains how to record this as contra-revenue.
Does Shopify charge extra if I don't use Shopify Payments?
Yes. If you route payments through an external gateway on Shopify, Shopify adds its own transaction fee on top of the outside processor's fee, as covered in the A2X Shopify fees guide. Using Shopify Payments avoids that extra Shopify charge.
How much does a chargeback cost?
On Shopify Payments in the US, a dispute carries a $15 fee, refunded only if you win, per the A2X Shopify fees guide. Because a single chargeback can wipe out the margin on many clean orders, disputes belong in any honest comparison of gateway pricing.
Should I pick a gateway on price alone?
No. Match the pricing model to your basket size — the fixed per-transaction fee punishes low-ticket stores and barely touches high-ticket ones — and weigh checkout conversion, payout speed, and dispute handling alongside the rate. The cheapest advertised percentage is rarely the cheapest gateway once every fee is counted.