Shopify payment methods, cost-first.
Most payment-methods guides bury the cost. We lead with it. Here's what every common Shopify payment method actually costs you, where each wins, and how to design a payment mix that minimizes the total percentage you pay to processors and middlemen. Every rate below was read off the vendor's own pricing page on the review date and is cited.
Credit cards
- Fastest authorization
- Highest conversion
- Universal acceptance
- Chargeback protection for customer
- Most expensive of the everyday methods
- Chargeback fees
- Held funds during disputes
- Surcharging legal in most states (with rules)
Default checkout. Smaller orders where card fees are tolerable.
Digital wallets
- One-tap checkout
- Better mobile conversion
- Tokenized PAN (lower fraud)
- Apple/Google biometric auth
- Same underlying card rails, same cost
- Can bypass storefront JS surcharges
- Apple Pay sometimes excluded from extensions
High-mobile traffic. Pair with Cart Transform–based fee logic so wallet checkouts still apply your rules.
ACH bank transfer
- Cheapest US payment method
- Cap dominates on large orders
- No card chargebacks (returns instead)
- Stable for B2B
- 3–5 business day settlement
- Customer signup friction (one-time)
- Not native on Shopify (except Plus B2B)
Orders above $30. B2B. Custom/made-to-order. Recurring subscriptions.
BNPL / Pay-in-4
- Lifts AOV on large orders
- Conversion bump on $300+ items
- Credit risk sits with the BNPL provider
- Most expensive payment method
- Provider branding on agreement
- Customer signs up for third-party account
- Fee is usually not refunded on returns
High-AOV consumer where AOV lift more than offsets the fee. Or use FinanceLayer for merchant-held layaway.
Manual (invoice / check / wire)
- Lowest fees of any method
- Standard for B2B
- Outside checkout, no Shopify constraints
- Manual reconciliation
- High operational overhead
- Slow
- Easy to miss/lose track
Very large B2B orders. Net-30 invoice terms. Wire transfers above $10K.
What does each payment method cost on Shopify?
Per-order cost on a Shopify store ranges from about 0.8% for an ACH bank transfer to about 6% for a third-party BNPL plan, a spread of more than five percentage points on the same order. Card rates also move with your Shopify plan: 2.9% + 30¢ on Basic, 2.7% + 30¢ on Grow, 2.5% + 30¢ on Advanced. Two of the numbers merchants most want, Shopify Plus card rates and the Shop Pay Installments merchant fee, are not published by Shopify at all.
| Method | Published rate | Notes | Source |
|---|---|---|---|
| Shopify Payments, Basic plan ($29/mo) | 2.9% + 30¢ | Online card rate. In person: 2.6% + 10¢. | [1] |
| Shopify Payments, Grow plan ($79/mo) | 2.7% + 30¢ | Online card rate. In person: 2.5% + 10¢. | [1] |
| Shopify Payments, Advanced plan ($299/mo) | 2.5% + 30¢ | Online card rate. In person: 2.4% + 10¢. | [1] |
| Shopify Payments, Plus plan (from $2,300/mo) | Not published | Shopify lists "most competitive rates" rather than a number. Negotiated. | [1] |
| Shop Pay | Your Shopify Payments rate | Part of Shopify Payments; no separate charge for the accelerated checkout. | [2] |
| Shop Pay Installments | Not published | Shopify does not publish the merchant fee. The fee is not returned on refunds. | [3] |
| PayPal Checkout | 3.49% + $0.49 | US domestic commercial transaction rate. | [4] |
| PayPal Pay Later | 4.99% + $0.49 | US domestic. Higher than PayPal’s own standard checkout rate. | [4] |
| Pay with Venmo | 3.49% + $0.49 | US domestic, same as PayPal Checkout. | [4] |
| ACH via Stripe | 0.8%, capped at $5.00 | The cap binds at $625. Above that the effective rate keeps falling. | [5] |
| Afterpay (via Square) | 6% + 30¢ | Square publishes a fixed rate: online and in person are identical. | [6] |
| Shopify third-party gateway fee | 2% / 1% / 0.6% / 0.2% | Basic / Grow / Advanced / Plus. Charged on top of the provider’s own fee. | [1] |
- [1] shopify.com/pricing (retrieved August 25, 2026).
- [2] Shopify Help Center: Shop Pay (retrieved August 25, 2026).
- [3] Shopify Help Center: Shop Pay Installments FAQ (retrieved August 25, 2026).
- [4] PayPal merchant fees (retrieved August 25, 2026).
- [5] stripe.com/pricing (retrieved August 25, 2026).
- [6] Square Support: Square fees (retrieved August 25, 2026).
Rates are US domestic and change without notice. Klarna, Affirm and Afterpay do not publish a standard US merchant rate on their own sites; the Afterpay row above uses Square's published seller rate because Square is one of the few platforms that states a fixed number. Read the BNPL row as a published-list-price indication, not as what a negotiated enterprise contract looks like.
The same $120 order, seven ways: what do you actually keep?
On a $120 order you keep $119.04 if the customer pays by ACH and $112.50 if they pay with Afterpay at Square's published rate, a difference of $6.54, or 5.45% of the order. Your Shopify plan moves the card number by 48¢ across the range from Basic to Advanced. The payment method matters several times more than the plan.
| Payment method | Fee | You keep |
|---|---|---|
| ACH via Stripe (0.8%, capped $5) | $0.96 | $119.04 |
| Shopify Payments, Advanced (2.5% + 30¢) | $3.30 | $116.70 |
| Shopify Payments, Grow (2.7% + 30¢) | $3.54 | $116.46 |
| Shopify Payments / Shop Pay, Basic (2.9% + 30¢) | $3.78 | $116.22 |
| PayPal Checkout (3.49% + 49¢) | $4.68 | $115.32 |
| PayPal Pay Later (4.99% + 49¢) | $6.48 | $113.52 |
| Afterpay via Square (6% + 30¢) | $7.50 | $112.50 |
Arithmetic only: each fee is the published rate applied to a $120 order, with no negotiated pricing, no chargeback costs, and no plan subscription allocated. Shop Pay is shown on the Basic line because Shop Pay processes at whatever your Shopify Payments rate is. Shop Pay Installments is absent because Shopify does not publish its merchant fee, and we will not put a number in a table we could not read off a vendor page.
One more line that does not appear above: if you accept payment through a third-party gateway instead of Shopify Payments, Shopify adds its own transaction fee on top, 2% on Basic down to 0.2% on Plus. On this order that is another $2.40 on Basic. Shopify's help documentation lists Shopify Payments, Shop Pay, Shop Pay Installments, PayPal Express Checkout and manual methods such as bank transfer as exempt from that fee when Shopify Payments is active, which is why a payment link that runs beside checkout does not trigger it.
What's the cheapest way to accept payments on Shopify?
ACH bank transfer, at 0.8% capped at $5.00 through Stripe. It is cheaper than every card method at any order value above roughly $30, and the $5 cap means the effective rate keeps falling as orders get bigger, 0.4% at $1,250, 0.1% at $5,000. The catch is settlement: 3–5 business days instead of instant, plus a one-time bank-connection step for the customer.
After ACH, the ranking is straightforward and mostly boring:
- ACH bank transfer, 0.8% capped at $5.
- Shopify Payments cards at whatever rate your plan buys, 2.5%–2.9% + 30¢.
- PayPal Checkout / Venmo, 3.49% + 49¢.
- BNPL, from 4.99% + 49¢ (PayPal Pay Later) to 6% + 30¢ (Afterpay at Square's published rate).
A question that comes up constantly: is it worth upgrading your Shopify plan to get a better card rate? That is pure arithmetic, and the break-evens are high.
- Basic → Grow costs $50/mo more and saves 0.2% per card order. Break-even: $25,000/mo in card volume.
- Basic → Advanced costs $270/mo more and saves 0.4%. Break-even: $67,500/mo.
- Grow → Advanced costs $220/mo more and saves 0.2%. Break-even: $110,000/mo.
Below those thresholds the plan upgrade is a feature purchase, not a payments optimization. Shifting even a modest share of orders from cards to ACH beats the plan upgrade at almost every volume level, because it changes the rate by two percentage points rather than a fraction of one.
How much does Shop Pay cost a merchant?
Shop Pay itself costs nothing extra. Shopify's help documentation describes Shop Pay as part of Shopify Payments, with transactions processed at your Shopify Payments rates, and Shop Pay orders are exempt from Shopify's third-party transaction fee. Shop Pay Installments is a different product with a separate merchant fee that Shopify does not publish.
The confusion is understandable, because the two products share a name and sit next to each other in the same checkout. They are economically very different:
- Shop Pay is an accelerated checkout. The buyer's details are already stored, so they check out in one tap. It runs on Shopify Payments and is billed at your Shopify Payments rate, 2.9% + 30¢ on Basic and so on down the plans.
- Shop Pay Installments is a buy-now-pay-later product financed by Affirm. Shopify does not publish the merchant fee. What Shopify's FAQ does confirm is that the fee behaves like a BNPL fee rather than a card fee: "The Shop Pay Installments transaction fee isn't returned to you when you issue a refund." The FAQ also limits eligible orders to $35–$30,000 USD or CAD.
That non-refundable-fee detail is the one to internalize. On a card sale, a full refund usually returns most of the percentage fee. On an installment sale it does not, so a product with a high return rate carries a materially higher effective BNPL cost than the headline rate suggests.
There is a second, quieter cost to Shop Pay that has nothing to do with its rate: it is an express checkout. Buyers can jump from a product page straight to payment authorization without your storefront JavaScript running. If you charge a card surcharge implemented in theme code, those orders arrive without the fee. Our surcharge guide covers how to close that gap.
How do I choose? A three-variable framework
Three numbers decide your payment mix: average order value, gross margin, and repeat-purchase rate. AOV tells you whether the fixed 30¢ or the percentage dominates. Margin tells you how much of your profit a percentage fee actually consumes. Repeat rate tells you whether it is worth spending one-time onboarding friction to move a customer onto a cheaper rail.
Average order value
Below about $30 the flat per-transaction fee dominates and every method converges; optimize for conversion, not cost. From $30 to $625 the ACH advantage grows linearly with order size. Above $625 Stripe's $5 ACH cap binds and the saving grows without limit.
Gross margin
A fee is a percentage of revenue but it is paid out of profit. On a $120 order at 60% gross margin, a 6% BNPL fee eats about 10% of your gross profit. On the same order at 20% margin it eats about 31%. Low-margin catalogs cannot afford BNPL economics no matter what it does to AOV.
Repeat-purchase rate
Connecting a bank account is a one-time cost paid by the customer. If they buy from you four times a year, you pay that friction once and collect the 2%+ saving four times. For one-and-done purchases the friction is charged against a single order and rarely pays for itself.
- Low AOV, any margin, low repeat: cards only. Do not add friction to save cents.
- High AOV, healthy margin, low repeat: cards by default, ACH offered prominently, a surcharge if your states allow it.
- High AOV, thin margin, high repeat (classic B2B): ACH first, cards as the fallback, and make the fee-free path the obvious one.
- High AOV, healthy margin, and customers who need to spread payments: compare third-party BNPL against merchant-held layaway before you accept a 5–6% cut.
How to design your payment mix
The ideal payment mix depends on your AOV, customer mix, and tolerance for settlement timing. A useful rule of thumb:
- Default to cards for orders under $30, the flat $0.30 fee dominates ACH, and conversion friction kills the value of trying to shift method.
- Steer to ACH for orders over $30, explicit "Pay by bank transfer" callout, especially for B2B and high-AOV.
- Surcharge cards wherever it's legal, recovers the cost of customers who insist on cards. Pair with ACH so the customer always has a fee-free option.
- Avoid third-party BNPL on orders where AOV lift doesn't offset the cost. Use FinanceLayer for merchant-held layaway instead.
- Reserve manual for very large B2B orders where the operational overhead is justified.
The MerchantLayer answer
MerchantLayer is three modules that, used together, take a Shopify merchant from a 6–9% percentages problem to sub-1%:
- FeeLayer passes the card processing cost to customers (where legal), shrinking the effective cost of card payments.
- PayLayer adds consumer ACH on every Shopify plan, so customers have a fee-free option.
- FinanceLayer lets you offer merchant-held layaway as an alternative to BNPL providers on high-AOV orders, you hold the goods until the customer finishes paying.
Combined cost: $42.98/mo flat. No volume caps, no percentage cuts, no tiered upgrades.
Pricing shown throughout this guide is US domestic list pricing as published by each vendor on August 25, 2026 and is subject to change. Negotiated rates, interchange-plus arrangements, and enterprise contracts will differ. This guide is informational and is not financial advice.