If you’re weighing Shopify vs WooCommerce payment plugins, one fee decides most of it. Use another gateway and Shopify adds 2% on Basic, 1% on Grow or 0.6% on Advanced. WooCommerce adds no platform fee, but you’ll need a plugin for installments.
Here’s the cost on a $100 sale.
| Feature | Shopify | WooCommerce |
|---|---|---|
| Built-in gateway | Shopify Payments | WooPayments |
| Fee for outside gateways | 2% / 1% / 0.6% by plan | None from the platform |
| US online card rate | 2.9% + 30ยข (Basic) to 2.5% + 30ยข (Advanced) | 2.9% + 30ยข with WooPayments |
| Built-in installments | Shop Pay Installments (powered by Affirm) | None. Add a plugin |
| Gateway choice | 100+ third-party providers | Wide, through extensions |
What is the difference between Shopify and WooCommerce payment plugins?
Shopify Payments runs on a closed model. Shopify Payments is built in. Every other provider connects as a third-party gateway.
WooCommerce works the other way. You add each gateway as a plugin, and WooPayments is the official one.
WooCommerce vs Shopify Payments: How payments work on Shopify
Shopify Payments handles cards, Shop Pay and payouts in one dashboard. Shopify also supports more than 100 other payment options, including PayPal, Stripe, Amazon Pay and Apple Pay.
Shopify Payments isn’t available in every country. Merchants in those countries have to use a third-party provider and pay Shopify’s extra fee.
WooCommerce vs Shopify Payments: How payments work on WooCommerce
WooPayments is a free plugin. It has no setup fee and no monthly fee for online payments. US cards cost 2.9% + 30ยข, and cards issued outside the US cost 1% more.
You can swap it for Stripe, PayPal, Square or Authorize.net. Your gateway sets your rate. WooCommerce sets nothing on top.
Shopify and WooCommerce payment plugins: Which platform has lower payment processing fees?
On the platform’s own gateway, both cost the same. In the US, Shopify Payments on Basic and WooPayments both charge 2.9% + 30ยข per online card sale. The gap opens when you use a different gateway.
- Shopify adds a surcharge. WooCommerce doesn’t.
Here is a $100 online card sale, US card, standard rates:
| Setup | Gateway fee | Platform surcharge | Total |
|---|---|---|---|
| Shopify Basic + Shopify Payments | $3.20 | $0 | $3.20 |
| Shopify Basic + Stripe | $3.20 | $2.00 | $5.20 |
| Shopify Grow + Stripe | $3.20 | $1.00 | $4.20 |
| Shopify Advanced + Stripe | $3.20 | $0.60 | $3.80 |
| WooCommerce + WooPayments or Stripe | $3.20 | $0 | $3.20 |
Plan price, hosting and plugin costs aren’t in this table. Shopify Payments rates also drop on higher plans, to 2.7% + 30ยข on Grow and 2.5% + 30ยข on Advanced.
Chargeback fees are the same on both. WooPayments and Shopify Payments each charge $15 per dispute in the US, and both refund it if you win.
Shopify and WooCommerce payment plugins fee comparison
Fee tables list rates. They rarely show what the rates do to a real month. These three calculations use the published rates above.
1. The surcharge in dollars per year
Take a store with 100 orders a month at $100 each. That is $10,000 in monthly sales.
- Shopify Basic with an outside gateway: $200 extra per month, or $2,400 a year.
- Shopify Grow: $100 extra per month.
- Shopify Advanced: $60 extra per month.
- WooCommerce: $0 extra from the platform.
There is a break-even too. On Basic, Shopify Payments charges 2.9% and the surcharge is 2%. An outside gateway would need a percentage rate below 0.9% to cost less. Standard processors don’t charge that little.
2. The fixed fee on every installment
Most gateways charge 30ยข per transaction. On a payment plan where each installment is a separate card charge, that fee repeats.
Take a $200 order paid in four $50 installments at 2.9% + 30ยข:
- One payment: $5.80 + $0.30 = $6.10 (3.05% of the order).
- Four installments: $5.80 + $1.20 = $7.00 (3.5% of the order).
The extra cost is $0.90 per order. It grows if your plan has more installments or your orders are smaller.
3. How much bigger a BNPL order must be
Buy now pay later fees are higher than card fees. Shop Pay Installments is commonly cited at 5.9% + 30ยข. WooPayments lists Klarna at 5.99% + 30ยข and Affirm or Afterpay at 6.0% + 30ยข, according to one fee guide dated October 2026.
Use this formula to find the break-even:
Required order increase = (BNPL % โ card %) รท (1 โ BNPL %)
With 5.9% against 2.9%, that is 3 รท 94.1, or about 3.2%. On a $200 average order, a BNPL customer has to spend about $206.38 for you to net the same as a card customer.
Returns change the math.
- The Shop Pay Installments fee isn’t refunded when you refund the order. A store with a high return rate needs a bigger lift.
Can you offer payment plans and BNPL on Shopify and WooCommerce?
Yes, on both, in different ways.
- Shopify has Shop Pay Installments, a buy now, pay later option powered by Affirm.ย
- WooCommerce has no built-in payment plans, so you add a plugin for WooCommerce deposits or scheduled installments.
Shopify: Shop Pay Installments and apps
Shopify’s Help Center sets these rules for Shop Pay Installments:
- Your business is based in the United States and sells in USD.
- Shopify Payments and Shop Pay are both active.
- The order total is between $50 and $20,000.
- The customer has a US billing address and a Shop Pay account.
Affirm can suspend your account for some store types. The Help Center lists primarily B2B businesses and password-protected stores among the reasons.
You get the full order amount, minus the fee, in 1 to 3 business days. Affirm carries the credit risk.
Shopify doesn’t publish the fee. You find your rate in the admin. The fee applies once per order, not once per installment.
Shopify merchants who need other plan types use third-party apps. Some Shopify apps support plans on any payment method the store accepts.
WooCommerce: deposit and payment plan plugins
A deposit takes part of the price at checkout. A payment plan splits the price across scheduled payments. Plugins can do either.
Some WooCommerce plugins charge later installments automatically. The WooCommerce.com Deposit and Payment Plans for WooCommerce plugin does this through the Stripe and PayPal. Check this feature for any plugin you test.
You set the terms and you collect the money. That also means you carry the risk of a failed payment.
Shop Pay Installments vs a merchant-run plan
| Condition | Shop Pay Installments | Payment plan plugin on WooCommerce |
|---|---|---|
| Who sets the terms | Affirm | You |
| When you get paid | Full amount less fee, in 1 to 3 business days | As each installment is collected |
| Who carries missed payments | Affirm | You |
| Typical cost | One higher fee per order (commonly cited 5.9% + 30ยข) | Gateway rate on each charge (2.9% + 30ยข on US cards with WooPayments) |
| Limits | US merchants, USD, orders of $50 to $20,000 | Set by the plugin and gateway |
WooPayments also supports BNPL methods such as Klarna, Affirm, and Afterpay. Their fees are higher than card fees, so confirm the current schedule in your WooPayments settings.
You can compare more options in our guide to the best BNPL plugins for WooCommerce.
WooCommerce vs Shopify Plugins: Which platform should you choose for payments?
Pick by your situation, not by the longer feature list.
| Your situation | Better fit |
|---|---|
| US store, orders of $50 to $20,000, want one dashboard | Shopify with Shopify Payments and Shop Pay Installments |
| You need a gateway Shopify Payments doesn’t replace | WooCommerce |
| You hold a negotiated processing rate | WooCommerce, since no platform surcharge sits on top |
| High-ticket products or deposits | WooCommerce with a payment plan plugin |
| Mostly B2B sales | WooCommerce with a payment plan plugin, since Shop Pay Installments can be suspended for B2B businesses |
If you already run WooCommerce, you don’t need to switch platforms to offer installments. You need a gateway and a plan plugin.
How do you set up installment payments on WooCommerce?
Setup takes six steps.
- Install a gateway. Use WooPayments or Stripe. Confirm it can save cards.
- Install a payment plan or deposit plugin. Review the WooCommerce payment plan plugin.
- Create the plan. Set the deposit, the number of installments and the interval.
- Check auto-charge. Confirm the plugin charges saved cards on your gateway.
- Run a test order. Test the first payment, a later installment and a failed payment.
- Show the schedule at checkout. Customers should see each date and amount before they pay.
