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.
Credit cards
- Fastest authorization
- Highest conversion
- Universal acceptance
- Chargeback protection for customer
- Most expensive
- 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 chargeback risk (return-only)
- Stable for B2B
- 1–3 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
- Risk on the BNPL provider, not you
- Most expensive payment method
- Provider branding on agreement
- Customer signs up for third-party account
- Stacks on top of card costs
High-AOV consumer where AOV lift more than offsets the 4–6% cost. Or use FinanceLayer for merchant-funded version.
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.
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 4–6% 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.