What's the cheapest way for an e-commerce store to accept bank payments?

The cheapest way for a US e-commerce store to accept bank payments is pay by bank with instant account linking. The customer logs in to their bank at checkout, the account is verified on the spot, and the payment carries no card interchange. It beats typed-in ACH and micro-deposits on total cost because it cuts the returns and abandoned checkouts that erase a low fee.

An online card sale costs a US merchant about 2.31% plus $0.25 under interchange-plus pricing, based on Helcim's 2026 averages reported by The Motley Fool. A store that adds a bank payment option to avoid that fee still loses the savings if returned payments, abandoned checkouts, and manual reconciliation eat them. The cheapest option is the one with the lowest total cost.

For the head-to-head fee math against cards, see Pay by bank vs. credit cards: which costs merchants less? This guide compares bank payment methods against each other and shows how to set one up without giving the savings back.

What are your options for accepting bank payments?

A US online store has four realistic ways to take money directly from a customer's bank account.

A fifth option, Request for Payment on the RTP network, lets a store ask the customer to push an instant payment from their bank. It removes return risk because the payment is final, but support depends on whether the customer's bank offers it, according to The Clearing House. For how it works, see Request for Payment (RfP): How to enable instant pay-ins.

What does accepting bank payments cost a store?

The total cost of acceptance has six parts, and the processing fee is only one of them.

• Processing fee. The per-transaction or percentage fee your provider charges. This is the number a fee comparison shows.
• Return losses. A customer's bank has up to 60 days after settlement to return a debit the customer says they didn't authorize, under Nacha's rules. A return that arrives after the order ships costs you the goods.
• Failed-payment operations. Every return or failed payment means someone chasing the customer, retrying, or writing it off.
• Verification cost. Micro-deposits cost money to send and cost sales while customers wait. Unverified accounts cost more in returns.
• Checkout drop-off. If paying by bank is harder than paying by card, customers abandon the cart, and a lost sale costs more than any fee.
• Settlement delay. Waiting days for funds ties up cash you could use for inventory or ads.

A method with a low fee and high returns costs more than one with a slightly higher fee and almost no returns, which makes “cheapest” a total-cost question.

How do you keep bank payment costs low?

Four decisions set the total cost of bank payments.

• Verify the account at checkout, not later. Instant bank linking confirms the account is real and belongs to the customer before the payment is sent, which cuts both returns and drop-off. Users link and verify a bank account in under 10 seconds with Aerosync, Aeropay's bank-linking product.
• Check risk before the payment settles. Returns are hard to recover once the order has shipped. A risk check before settlement lets you approve trusted customers quickly and stop risky payments early. For recovery steps when a payment does fail, see How do you recover a failed bank payment?
• Know who carries the return. Ask every provider whether a returned ACH payment comes out of your balance or theirs. Aeropay Guaranteed ACH, for example, covers eligible bank-initiated returns, across 50+ return types including insufficient funds, up to the merchant's agreed coverage limit.
• Make it the easy option. Show pay by bank next to cards with a one-line reason to choose it. Should e-commerce merchants offer pay by bank? covers placement and incentives.

What should you ask a bank payment provider about cost?

Ask each provider these eight questions before you sign.

1. What is the all-in cost per transaction, including return and failed-payment fees?
2. Do you guarantee ACH payments, and what does the guarantee cover?
3. How do customers verify their account, and how long does it take at checkout?
4. How many US banks and credit unions can customers connect to?
5. What risk checks run before a payment is submitted?
6. How fast do funds settle, and is same-day or real-time settlement available?
7. Can the same integration handle refunds and payouts?
8. What platforms and checkout tools do you integrate with today?

How to choose a pay by bank provider in the US goes deeper on provider evaluation.

Frequently asked questions

Is ACH cheaper than credit cards for e-commerce?

Yes, on the processing fee. An online card sale costs a US merchant about 2.31% plus $0.25, and a bank payment carries no card interchange. The total cost stays lower when the store verifies accounts at checkout and its provider covers returned payments.

What's the cheapest way to accept bank payments with no fees at all?

A manual bank transfer avoids a processor fee. It moves the cost to staff time spent matching payments to orders, slower fulfillment, and sales lost when customers leave the site to send the money.

Do customers need to know their account number to pay by bank?

Not with instant bank linking. The customer logs in with their own bank, the bank issues a secure token, and the store never sees their password.

Which bank payment method costs an online store the least?

The cheapest way for a US e-commerce store to accept bank payments is pay by bank with instant account verification, because it keeps fees low without letting returns and checkout drop-off eat the savings. Judge every option on total cost of acceptance, and ask who carries the return before you compare fees.

See what pay by bank would cut from your processing costs.