Shopify and BigCommerce both charge you a percentage of every order for the privilege of not using their in-house payment gateway, and on their entry plans that percentage is 2%. That is larger than the entire rate advantage most merchants are chasing when they go shopping for a processor. On Shopify Basic, an outside gateway has to come in under about 1.3% all-in to beat Shopify Payments' 3.3%, which is not a rate that exists in ordinary card-not-present retail. The comparison below sets out both platforms' published numbers, the one exemption on BigCommerce that changes the answer completely, and the three situations where paying the penalty is still the right call.
The published numbers, side by side
Methodology: plan prices, card rates and penalty percentages are taken from each company's own pricing and billing documentation, all opened 27 July 2026. Shopify's card rates are its online standard rates for the United States. BigCommerce's structure is the one that took effect on 1 June 2026 with 60 days' notice. Where a figure is not published, the cell says so rather than guessing.
| Plan | Monthly (annual billing) | In-house card rate | Fee for an outside gateway |
|---|---|---|---|
| Shopify Basic | $39 ($29) | 2.9% + 30c | 2% |
| Shopify Grow | $105 ($79) | 2.7% + 30c | 1% |
| Shopify Advanced | $399 ($299) | 2.5% + 30c | 0.6% |
| Shopify Plus | From $2,300 | Not published | 0.2%, waived if Shopify Payments is the sole provider |
| BigCommerce Core | $39 ($29) | Varies by embedded provider | 2.0% |
| BigCommerce Growth | $105 ($79) | Varies by embedded provider | 1.0% |
| BigCommerce Scale | $399 ($299) | Varies by embedded provider | 0.6% |
| BigCommerce Performance | From $1,499 | Varies by embedded provider | None under contract |
Sources: Shopify's pricing page and its third-party transaction fees documentation; BigCommerce's 2026 plan and pricing update.
What the fee is actually charged on
This detail is worth more than the headline percentage. Shopify's documentation gives the formula: "[(cost of products - discounts) + tax + shipping charges] x rate", assessed over a 30-day period. The fee therefore applies to sales tax and shipping revenue, neither of which is margin you keep. On a $80 order with $6 tax and $8 shipping, the 2% is charged on $94, not on the $80.
Shopify also exempts several methods when Shopify Payments is active on the store: Shopify Payments itself, Shop Pay, Shop Pay Installments, "Paypal Express Checkout", and "Manual payment methods such as cash, cash on delivery (COD), and bank transfers". Stores created after 12 May 2025 also pay the fee on store credit and gift card redemptions, which is a change many merchants have not noticed. Plus stores that use Shopify Payments as their sole provider have the fee waived entirely, gift cards included.
BigCommerce works differently and the difference matters. Its fee is decided per order, based on which provider processed that order. Providers on its embedded list carry no fee at all, and the list is broad: the announcement names Adyen, Affirm, Afterpay, Amazon Pay, BigCommerce Payments, Checkout.com, Klarna, PayPal Braintree, PayPal Complete Payments, PayPal Wallet, Stripe and Worldpay among others. An Open Payment Provider is defined as "Any payment provider not on this list". So a BigCommerce merchant running Stripe pays no penalty, while a Shopify merchant running the same Stripe account pays 2% on Basic. Same processor, opposite outcome.
The arithmetic, ours
Take a store doing $20,000 a month across 250 orders at an $80 average, on Shopify Basic, and compare Shopify Payments against a negotiated outside gateway at 2.5% plus 25 cents. That gateway is 0.4 percentage points cheaper on paper.
- Shopify Payments: 2.9% of $20,000 is $580, plus 250 transactions at 30 cents is $75. Total $655, an effective 3.28%.
- Outside gateway: 2.5% of $20,000 is $500, plus 250 at 25 cents is $62.50, so $562.50 in processing. Then Shopify's 2% on the same volume adds $400. Total $962.50, an effective 4.81%.
The cheaper processor costs $307.50 more per month. To break even, the outside gateway would have to keep its own cost under $255 on $20,000 of volume, which is 1.28% all-in. No mainstream card-not-present processor prices there.
The higher plans change the threshold but not the conclusion for most stores. On Grow, with a 1% penalty and a 2.7% in-house rate, the outside gateway needs to land under about 2.08% all-in. On Advanced, with a 0.6% penalty against 2.5%, it needs to beat about 2.28%. That last one is genuinely reachable for a merchant with an established interchange-plus merchant account, which is the point at which this decision stops being theoretical.
One more calculation people get wrong: upgrading a plan to reduce the penalty. Moving from Basic to Advanced cuts the penalty by 1.4 points but costs $360 more per month at monthly billing. That trade only pays above roughly $25,700 of monthly volume processed through the outside gateway, before you count the improvement in Shopify's own card rate. Below that number you are paying $360 to save less than $360.
Three reasons to pay the penalty anyway
The fee is designed to keep you on the in-house rail, and usually it should. But there are cases where the outside gateway is not optional:
- Underwriting. In-house payment products decline whole categories. If your products fall outside what Shopify Payments or BigCommerce Payments will underwrite, the penalty is not a choice you are making, it is the cost of being in your category. Price it into your margins rather than arguing with it. What that constraint looks like from the merchant's side is the subject of our piece on holds and reserves.
- Country availability. In-house gateways are not offered everywhere, and a merchant in an unsupported country has one route. The comparison then is not gateway versus gateway, it is platform versus platform, and BigCommerce's exempt-provider list becomes a genuine reason to prefer it.
- An existing merchant account below the threshold. If you already hold interchange-plus pricing that lands under about 2.3% all-in and you are on Shopify Advanced or higher, run the numbers, because you may be one of the few merchants for whom the outside route wins. Get your effective rate in writing from your processor first, including assessments and monthly minimums, not the headline rate from the sales call.
What to check before you switch anything
Pull last month's statement and compute your true effective rate: total fees divided by total card volume, including monthly minimums, gateway fees, chargeback fees and statement fees. Compare that single number, not the advertised rate, against the in-house rate plus zero penalty. Then look at where else the platform is taking a percentage, because payment fees are rarely the largest line: dispute fees and returns handling often are.
Two things we could not settle this run and will not assert. Wix's pricing pages were unreachable, so Wix is not in the table. And Squarespace's pricing page publishes a 2% online store transaction fee on its Starter plan and 0% on Business, Commerce and Advanced Commerce when using Squarespace Payments, but does not state on that page whether the fee differs when a merchant uses Stripe or PayPal instead. If you are on Squarespace, ask support in writing before you plan around it.
The broader habit is worth keeping. A payment penalty is one of several levers a platform holds over your economics, and it can be changed with notice, as BigCommerce just demonstrated with 60 days. Knowing which levers exist, and what each one is worth annually, is the exercise in our platform dependency audit. If a 2% fee decides whether your store is profitable, the fee is not the problem you have.
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