Best eCheck Payment Services for Small Businesses

The cheapest way for most small businesses to accept eCheck (ACH) payments is GoCardless (0.5% + $0.05, capped at $5) or Helcim (0.5% + $0.25, capped at $6). Stripe (0.8%, capped at $5) is the easiest if you already sell online, and Square or QuickBooks Payments (1%) make sense if you already invoice through them. On payments over about $600, the capped services all cost roughly $5 — so pick by platform fit, not fees. All rates below come from each provider’s own pricing page.

Which eCheck service is cheapest?

Run the math on your typical payment size, because the caps change the answer:

• On a $200 invoice: GoCardless $1.05, Helcim $1.25, Stripe $1.60, Square $2.00. Percentage rate wins — GoCardless and Helcim are cheapest.
• On a $1,000 invoice: GoCardless $5 (capped), Stripe $5 (capped), PayPal $5 (capped), Helcim $5.25, Square $10. The caps kick in and almost everything costs about $5.
• Add the monthly fees: Authorize.net’s 0.75% rate looks low, but the $25 gateway fee plus $10 eCheck minimum means you need real volume before it beats a $0-monthly service.

Every option here is far cheaper than card processing — a $1,000 card payment costs roughly $29 at typical 2.9% rates, versus about $5 by ACH. That gap is the whole reason to offer eCheck on large invoices. Setup steps are in our guide to accepting eCheck payments as a business.

What about Melio and Bill.com?

They solve a different problem. Melio and Bill.com are bill-pay platforms — built for paying vendors and collecting invoices between businesses, not for taking customer payments at checkout. Melio sends standard ACH free within each plan’s monthly allotment (then $0.50 per payment) on plans from $0 to $80/month. Bill.com charges a flat $0.59 per ACH transaction on top of per-user plans from $49/user/month. If a customer asks “can I pay your invoice from my bank account?”, either works. If you need a Pay button on your website, use a processor from the table instead.

What if your business is high-risk?

Mainstream processors underwrite conservatively — CBD, supplements, credit repair, subscription boxes with high refund rates, and similar categories get declined at Stripe or Square. High-risk specialists like PaymentCloud approve these merchants and support ACH/eCheck, but publish no rates; expect a sales call and pricing set to your risk profile. Dwolla serves platforms embedding ACH by API at scale — also quote-only, and not a plug-and-play checkout option.

Common problems

• Returns. An eCheck can bounce days after it “went through” (insufficient funds, closed account, revoked authorization). Most providers charge a return fee — $3 at Authorize.net, $5 at PaySimple. Ship goods after settlement, not after submission.
• Settlement speed. Standard ACH settles in 1–3 banking days. Same-day ACH exists but costs extra where offered. See how long an eCheck takes.
• Underwriting delays. Every provider verifies your business (EIN, ownership, expected volume) before enabling ACH. Apply before you need the money, not the week an invoice is due.

Not sure eCheck is the right rail at all? Start with eCheck vs ACH or the plain-English eCheck guide.

Rates checked on each provider’s published pricing page: GoCardless, Helcim, Stripe, PayPal, Square, Authorize.net, PaySimple, Melio, and Bill.com. Rates change — confirm on the provider’s page before signing up.

Other eCheck Accepted categories: