What's the best payment gateway for your online store in 2026?
Shopify, WooCommerce or PrestaShop: the gateway that costs you the least all in, depending on the platform your store runs on.
The short answer depends on your platform. On Shopify, stick with Shopify Payments: any other gateway triggers a surcharge of 2% per sale on Basic, 1% on Grow and 0.6% on Advanced, on top of that gateway's own fees. On WooCommerce or PrestaShop, there's no surcharge, so Stripe (2.9% + 30¢ per US card, no monthly fee) is the best all-round pick. Keep PayPal as a second button, and look at Mollie only if you sell mostly to European buyers. We compared five gateways on what a store owner really pays: card fees, platform surcharge, disputes, installments and the risk of a payout hold, with the full math for a store doing $10,000 a month.
The ranking is editorial: a sponsored spot is always labeled on its card, and no affiliate link changes a score.
The best pick for each platform
Your situation, your gateway
A store owner never picks a gateway in a vacuum: it plugs into a platform with its own rules and apps. Here's the shortcut before the detail on each tool.
Any other gateway adds 0.6% to 2% depending on your plan.
You sell on WooCommerce and you're starting outStripeNo monthly fee, the most-used plugin.
You sell a lot to European buyersMollieLocal European payment methods, priced in euros.
You process hundreds of thousands a monthAdyenInterchange++ pricing, on quote.
You want to offer installmentsShop Pay Installments or a BNPL appPrice it against your margin first.
You're worried about frozen fundsPayPal as a second button$0 until someone uses it.
The 5 ecommerce payment gateways compared
The full ranking. Scores match our general payment gateway ranking; here we also weigh what only hits an online store (the platform, disputes, installments). Prices come from official rate cards, for US cards unless shown in euros.
| Best for | Best feature for a store | Free plan | Team size | Visit | ||||
|---|---|---|---|---|---|---|---|---|
| 1 | Stripe | Best on WooCommerce | No monthly fee, deepest API | 4.0/5 | $0/mo + 2.9% + 30¢ | ✓ | WooCommerce, PrestaShop, custom stores | Visit → |
| 2 | Mollie | Best for selling into Europe | Local European payment methods | 3.9/5 | €0/mo + 1.80% + €0.25 | ✓ | Stores selling into Europe | Visit → |
| 3 | PayPal | Best backup checkout button | Buyers pay without typing a card | 3.4/5 | $0/mo + 3.49% + 49¢ | ✓ | Every store, as a backup | Visit → |
| 4 | Shopify Payments | Best on Shopify | No Shopify surcharge | 3.3/5 | 2.9% + 30¢ on Basic | — | Shopify stores only | Visit → |
| 5 | Adyen | Best for enterprise stores | Interchange++ pricing | 3.3/5 | Fixed fee + Interchange++ | — | Enterprise, marketplaces | Visit → |
Same scores on every page we publish, on five weighted criteria. Prices checked in 2026 on official pages.
How we compared and scored
A payment gateway takes your buyer's card at checkout, gets it approved by their bank and pays the money out to you. For an online store, its real cost has four layers: the card fee, any surcharge from your platform, dispute fees (when a buyer challenges a payment with their bank) and, if you offer it, the cost of installments. Most roundups stop at the first layer. We priced all four where the vendor publishes them.
We read rate cards and dispute policies on official pages in 2026, then merchant feedback on the Shopify Community and on WordPress plugin pages, starting with the worst: held funds, updates that break checkout, apps that are hard to set up. Stripe, Mollie, PayPal and Adyen keep the score from our general ranking. Shopify Payments gets its first score here, on the same five criteria and weights, and keeps it on our future pages. We didn't open accounts with these vendors: we compared what they publish and what their customers report.
Mentioned but not scored: WooPayments (its US rate card isn't in our research), Square Online and Authorize.net, and the installment specialists Affirm, Afterpay and Klarna, whose merchant fees we couldn't read on an official page.
- Per-payment feesPercentage and fixed fee per card type, plus any monthly plan.25%
- Integrations (platforms, API)Official apps for Shopify, WooCommerce and PrestaShop, API depth, payment methods.20%
- Payouts and cash flowFirst payout delay, schedule after that, payout fees.20%
- Freedom (plans, contracts)Monthly fee, commitment, minimum billing, plan requirements.20%
- Support and freeze riskReachable support, frozen accounts and held funds in recent reviews.15%
No affiliate link changes a score or a rank.
Stripe
In the US, Stripe charges 2.9% + 30¢ per successful card payment, with no setup or monthly fee. Add 1.5% for an international card, 1% if a currency conversion is needed, and 0.5% for a card typed in by hand. On WooCommerce, its official plugin has more than 700,000 active installs; PrestaShop has a module too.
What puts it first is the integration: its API (the interface your developer plugs into your site) is the most complete in this lineup, and Stripe Billing runs subscriptions for 0.7% of billed volume. To push each order into your CRM or your books, our Stripe and n8n guide covers the most useful automations.
The catch, for a store: on Shopify, Stripe counts as a third-party gateway, so you pay Shopify's surcharge on top ($200 a month at $10,000 in sales on Basic). On WooCommerce, merchants complain about plugin updates that change their settings, such as switching Link, Stripe's express checkout, back on after they had turned it off. Recheck your settings after every update. Accounts frozen over a dispute rate flagged as high also come up in reviews, so keep a second gateway live.
- No monthly fee, 2.9% + 30¢
- Official WooCommerce plugin, widely used
- Most complete API in the lineup
- Stripe Billing for subscriptions
- ✓Widest integration options
- ✓Full public rate card
- ✓No contract or monthly minimum
- ✗Shopify surcharge on top when used on Shopify
- ✗Plugin updates that change your settings
- ✗International cards cost 1.5% more
The best pick on WooCommerce and PrestaShop for most stores. Not the right pick on Shopify, where the surcharge pushes your bill up by more than half.
Mollie
Mollie is a Dutch gateway with no monthly fee and no contract, priced in euros: 1.80% + €0.25 for a consumer Visa or Mastercard issued in the European Economic Area (EEA), 2.90% + €0.25 for a business card or American Express. In France, it drops to 1.20% + €0.25 on Cartes Bancaires, the local card network. You choose your payout rhythm (daily, weekly or monthly) and the first five payouts each month are free.
Its score comes mostly from that European rate card and its apps: an official Shopify app, a free PrestaShop module and a WooCommerce plugin with more than 100,000 active installs. On disputes, Mollie charges a chargeback only if you lose it, though the amount isn't shown on its pricing page. Ask before you sign.
The catch: it's a European tool. A US store won't get these rates and doesn't need Cartes Bancaires. On WooCommerce, merchants report an update that took their site down and slow fixes, and reviews describe accounts frozen without explanation. On Shopify, Mollie is a third-party gateway, so the surcharge applies.
- Priced in euros, no monthly fee
- Free PrestaShop module
- Chargeback billed only if you lose
- Payout rhythm of your choice
- ✓Cheap on European cards
- ✓Apps for the three big platforms
- ✓No fee on disputes you win
- ✗Not built for US-only stores
- ✗WooCommerce updates sometimes risky
- ✗Chargeback amount not published
The right pick for a European store selling mostly in Europe. Not the right pick for a US-only store: Stripe covers you better there.
PayPal
In the US, PayPal Checkout (the yellow button) costs 3.49% + 49¢ per transaction. Advanced card processing, where buyers type their card on your own checkout, drops to 2.89% + 29¢. International transactions add 1.50%. Its fee score (2.8 out of 5) stays the same on every page we publish: it rates the standard yellow button, the most expensive everyday rate in this lineup, not the cheaper card option that takes more setup.
Why keep it? Because some buyers trust their PayPal account more than a new store with their card, and because a second live button keeps you selling the day your main gateway holds your funds. It plugs into Shopify, WooCommerce and PrestaShop. Our PayPal and Zapier guide shows how to send each sale into your other tools.
The catch: held funds. New sellers describe about three weeks of holds on their first sales, released within 24 hours once a tracking number was added. Add tracking to every order the day it ships.
- The button buyers recognize
- No monthly fee for PayPal Checkout
- Works on the three big platforms
- Costs nothing until it's used
- ✓Familiar to buyers
- ✓Easy backup option
- ✓Cheaper card option for small orders
- ✗3.49% + 49¢: highest standard rate
- ✗Holds on new seller accounts
- ✗49¢ fixed fee hurts small orders
Keep it as a second button on every store. Not the right pick as your only card gateway: at $10,000 a month, PayPal Checkout costs $447 against $350 at Stripe.
Shopify Payments
Shopify Payments is Shopify's built-in gateway. On US cards it charges 2.9% + 30¢ on the Basic plan, 2.7% on Grow and 2.5% on Advanced. Its real value is what it saves you: any other gateway on Shopify adds a surcharge of 2%, 1% or 0.6% per sale depending on your plan. Shop Pay Installments, its pay-over-time option run with Affirm, lives inside it too.
Why only 3.3 overall when it's our first pick on Shopify? Because our score rates a gateway for any store, and Shopify Payments only works on Shopify (3.0 on integrations) and needs a paid Shopify plan (3.4 on freedom). Its fees score 4.2: Stripe's rate on Basic, lower on higher plans. Its weakest point is held funds (2.4): on Shopify's forum, one merchant describes about $25,000 held with no reason given and released after 120 days.
The catch: no reason is required for a reserve, so a sales spike, a wave of disputes or long shipping times can tie up your cash. Export your order and customer data regularly and keep a second option live.
- No Shopify surcharge
- Rate drops with your Shopify plan
- Shop Pay Installments built in
- Managed from your Shopify admin
- ✓Cheapest option on Shopify, by far
- ✓Nothing extra to install
- ✓Lower rate on Grow and Advanced
- ✗Shopify only
- ✗Reserves of up to 120 days reported
- ✗Needs a paid Shopify plan
The default on Shopify. Not relevant anywhere else, and not a reason to drop your backup button: holds happen.
Adyen
Adyen doesn't publish a flat rate. You pay a fixed processing fee per payment (not published in dollars) plus the cost of the payment method. For Visa and Mastercard, that's Interchange++: the card-issuing bank's fee, the network's fee, then Adyen's margin, each shown separately. American Express costs 3.95%. There's no setup or monthly fee, but a minimum monthly billing can apply depending on your industry.
That model favors big volume: you pay each card's real cost instead of a blended rate that also covers the most expensive cards. 3D Secure, the extra check by the buyer's bank, adds no fee. What we can't do is price your bill at $10,000 a month without your interchange mix: ask for a simulation on your real sales.
The catch: Adyen isn't made for starting out. Minimum billing, negotiation, an unpublished payout delay and a developer to integrate it make it a tool for large teams.
- Interchange++: each cost shown separately
- No setup or monthly fee
- 3D Secure at no extra cost
- Built for high volume
- ✓Most transparent model at scale
- ✓Fits large retailers and marketplaces
- ✓No 3D Secure surcharge
- ✗Possible minimum billing
- ✗Bill hard to predict without a simulation
- ✗Payout delay not published
The right pick for an enterprise store that negotiates. Not for a store starting out: Stripe costs less and needs no contract.
What your gateway really costs at $10,000 a month
Take a store selling $10,000 a month with a $50 average order (200 orders), all on US cards. Our math, from official rate cards:
- Shopify Basic + Shopify Payments (2.9% + 30¢): $350.
- Shopify Basic + Stripe: $350 in Stripe fees + $200 Shopify surcharge (2%) = $550. On Grow, the surcharge drops to $100 ($450); on Advanced, to $60 ($410).
- WooCommerce or PrestaShop + Stripe: $350, no surcharge.
- PayPal Checkout alone (3.49% + 49¢): $447. With advanced card processing (2.89% + 29¢): $347.
The lesson: on Shopify, the surcharge outweighs any gap between gateways. A third-party gateway there only makes sense for a payment method Shopify Payments lacks. And if 20% of your sales come from international cards, Stripe adds $30 a month on top.
You're on Shopify
You're on WooCommerce
You sell into Europe
- Price your fees all in: gateway, platform surcharge, monthly plan.
- Ask what a dispute costs and whether it's refunded when you win.
- Keep a second gateway live and ready.
- Add tracking to every order you ship.
- Test every payment plugin update on a staging copy.
- Export orders and customers regularly.
Shopify surcharge, disputes, installments, held funds: the traps of an online store
Roundups stop at the card rate. Store owners talk about the surcharge they missed, the dispute fee, the installment cost eating their margin and money held for months. Here are seven points from their feedback and official rate cards.
Shopify's surcharge on third-party gateways
ShopifyOn Shopify, any gateway other than Shopify Payments triggers a surcharge on each sale: 2% on Basic, 1% on Grow, 0.6% on Advanced, on top of that gateway's fees. A merchant on Shopify's forum found out after adding Klarna through Mollie: 2% to Shopify plus Klarna's own fee, and gave up.
Another common mix-up: support says Shopify Payments has "no fee", yet the merchant sees fees on every sale. Both are true: no surcharge, but processing fees. Get the breakdown in writing and compare total cost.
- Basic / Grow / Advanced
- 2% / 1% / 0.6%
Disputes: know the fee before the first one
DisputesA dispute (or chargeback) is a buyer challenging a payment with their bank. Each gateway bills it differently, and some keep part of the fee even when you win. Mollie bills a chargeback only when you lose it. With Shop Pay Installments, Affirm handles disputes for up to 60 days, and fees aren't returned when you refund.
Ask your gateway in writing: what does a dispute cost, and is it refunded if you win? Then build a standard reply pack: invoice, proof of delivery with tracking, messages with the buyer.
- Mollie
- Billed only if you lose
Installments: price them against your margin
ConversionPay-over-time options reassure buyers on big orders, but they cost far more than a card. Shop Pay Installments, run with Affirm, doesn't publish its merchant fee on the pages we read, and neither do Afterpay or Klarna for US merchants.
Ask for the rate in writing and compare it with your margin per order. On Shopify, run installments through Shopify Payments when you can, so the third-party surcharge doesn't stack on top.
- Merchant fee
- Not published: ask in writing
Keep a backup gateway live
Cash flowOn Shopify's forum, one merchant describes about $25,000 held by Shopify Payments with no reason given, released after 120 days. The pattern repeats at Stripe, PayPal and Mollie: a sales spike, a few disputes, long shipping times, and the gateway sets money aside.
Your defense: two live payment options at once, export your orders and customers regularly, warn your gateway before a big promotion, and pay out your balance often.
- Reported reserve
- 120 days
Test plugin updates before they go live
WooCommerceReviews of the Stripe and Mollie plugins for WooCommerce tell the same story: an update that changes a setting, or takes the site down. A store without checkout on a sale day is the scenario to avoid.
Turn off auto-updates for your payment plugin, test each version on a staging copy, and place a test order before going live.
- Habit
- Staging test before each update
Release held funds with tracking numbers
PayPalOn a new account, PayPal often holds the money from your first sales. Sellers describe about three weeks of holds, released within 24 hours once the tracking number was added. Long shipping times also feature among the reasons Shopify Payments sets up a reserve.
Push tracking automatically from your platform the day each order ships. It also helps you win disputes.
- Hold released
- Within 24 h of tracking
Fixed fees hurt small orders
FeesOn a $10 order, Stripe's 30¢ fixed fee alone is 3% of the sale, and PayPal Checkout's 49¢ almost 5%. Add the percentage and you lose 5.9% to 8.4% of every small order.
If your average order is under $20, compare fixed fees first: PayPal advanced card processing, at 29¢, costs less than Stripe on small orders.
- On a $10 order
- 5.9% to 8.4% in fees
What you need around your store
The gateway takes the money. For the rest, here are our other rankings.
SaaS, freelancers, small businesses.
You're still picking your store platformEcommerce platformsWhat each platform takes from your sales.
You're opening a small storePlatforms for small storesOur picks to start lean.
You also sell at markets or in personCard readersTaking payments at the counter.
You're on Shopify and want to email buyersEmail marketing for ShopifyThe tools that plug in best.
You want to automate your Stripe ordersStripe and n8nSend each payment into your tools.
Ecommerce payment gateway · FAQ
Does Shopify charge a fee if I use Stripe or PayPal?
Yes for Stripe: any gateway other than Shopify Payments triggers a 2% surcharge on Basic, 1% on Grow and 0.6% on Advanced, on top of the gateway's fees. Check in your Shopify admin whether your PayPal button is affected. The surcharge shows on your Shopify bill, not your gateway statement, which is why it surprises people.
Shopify Payments or Stripe on Shopify?
Shopify Payments, in almost every case, because it avoids the surcharge: at $10,000 a month on Basic, Stripe direct costs you $200 more. Pick another gateway only for a payment method Shopify Payments doesn't offer in your country.
What's the best payment gateway for WooCommerce?
Stripe for most stores: 2.9% + 30¢, no monthly fee, and an official plugin with more than 700,000 active installs. Add PayPal next to it. Lock plugin auto-updates: merchants report updates that changed their checkout settings.
Why is my payment gateway holding my funds?
Because it rates your risk as too high: a sudden sales jump, disputes, long shipping times or a new store. The gateway then keeps a reserve, sometimes for months; one Shopify merchant reports 120 days. Answer document requests fast and in full, add tracking to every order, and route buyers to your backup gateway meanwhile.
Should my store have two payment gateways?
Yes. Shopify, WooCommerce and PrestaShop all show several payment options on the same checkout. PayPal Checkout has no monthly fee, so it costs nothing until it's used, and it keeps you selling if your main gateway holds your funds.
How much do buy now, pay later options cost a store?
More than a card, and US providers rarely publish the merchant rate: Shop Pay Installments, Affirm, Afterpay and Klarna all price it on request in the pages we read. Ask in writing, compare with your margin per order, and on Shopify run it through Shopify Payments to avoid the surcharge.
Do I need a merchant account for my online store?
No, not with Stripe, Shopify Payments or PayPal: they handle card acceptance themselves and you sign up online. A separate merchant account mostly makes sense at high volume, where a quote with Interchange++ pricing, like Adyen's, can beat a flat rate.
Get the next ranking in your inbox
New Labs rankings for online sellers, with real prices and the fees vendors leave out.