ACH is the cheapest way to get paid on a large invoice. Cards cost a percentage of every transaction, so a $10,000 invoice can cost you $250 or more in fees. ACH (bank-to-bank transfer) usually costs a flat fee or a small capped percentage, which is why B2B sellers, agencies, and anyone invoicing four and five-figure amounts prefer it.
The problem: QuickBooks makes you choose between Intuit's own processor and manual bank-transfer chasing. This guide shows a third option, collecting ACH on your QuickBooks invoices through a gateway you choose, with every payment recorded back against the invoice automatically.
Does QuickBooks Charge for ACH Payments?
Yes. If you use QuickBooks Payments (Intuit's native processor), ACH costs 1% per transaction, capped at $10. So a $500 invoice paid by ACH costs $5, and any invoice above $1,000 costs the flat $10 cap. Card payments through the same processor cost 2.99%.
That capped rate is competitive, but it comes with three catches:
US only. QuickBooks Payments ACH is not available outside the United States.
Intuit lock-in. You process through Intuit or not at all. If you already use Stripe, Authorize.net, or another gateway elsewhere in your business, you now run two payment stacks.
No bank payments over other channels. The native button only works inside the invoice. There is no way to take an ACH payment over the phone or via a link you send by text.
If those limits do not bother you, Intuit's native ACH is a reasonable option for invoice-only collection. For everything else, you can collect ACH through your own gateway instead.
Option 1: QuickBooks Payments (Intuit Native ACH)
Intuit's processor adds a "Pay Now" button to invoices that supports both card and ACH.
Pros:
Native, no extra setup beyond enabling
Auto-reconciliation built in
ACH capped at $10 per transaction
Limitations:
US only
You cannot use your existing gateway
ACH only works inside the QuickBooks invoice, not over the phone or via standalone links
One processor, one set of rates, no routing flexibility
Option 2: Collect ACH Through Your Own Gateway with Shuttle
Shuttle adds ACH collection to QuickBooks invoices through any gateway that supports ACH, such as Stripe or Authorize.net. You keep your existing processor, your existing rates, and your existing banking relationship. Shuttle is the layer that connects that gateway to QuickBooks and reconciles the payment.
Here is how it works:
Install the Shuttle QuickBooks Online Invoice Payments app
Connect the payment gateway you already use for ACH
Add a payment option to your QuickBooks invoices
Customers pay by bank transfer from the invoice
The payment is recorded against that invoice in QuickBooks automatically
No manual matching, no second payment stack, no switching processor. If your gateway supports ACH, Shuttle can collect it on your QuickBooks invoices.
Why route ACH through your own gateway
Keep your rates. If you have negotiated ACH pricing with your provider, you keep it.
One processor across the business. The same gateway handles your card, ACH, and other payments, so reconciliation and reporting stay in one place.
Not US-locked at the platform level. Your coverage follows your gateway, not Intuit's US-only ACH rule.
PCI DSS Level 1. Bank and card details are handled in a compliant environment.
ACH Over the Phone: Voice Payments
Most ACH-on-invoice tools stop at the invoice. Shuttle also collects ACH **over voice**, through Voice Checkout. A customer on a call can pay an invoice by bank transfer without reading card numbers aloud and without leaving the call to find a link.
This matters for businesses that still close and collect by phone: B2B sales, accounts-receivable teams chasing overdue invoices, field service, and contact centres. The agent confirms the invoice, the customer authorises the bank payment on the call, and the payment posts back to QuickBooks like any other. Card-only voice solutions cannot do this.
ACH vs Card on QuickBooks Invoices: Which to Use
Both have a place. The right choice depends on invoice size and customer.
Factor | ACH (bank transfer) | Card |
|---|---|---|
Cost on large invoices | Low (flat or capped) | High (percentage of total) |
Settlement speed | 1 to 4 business days | Often same or next day |
Best for | B2B, large invoices, recurring billing | Smaller invoices, consumer, instant need |
Customer friction | Bank details once, low after | Card details each time unless saved |
Chargeback profile | Lower | Higher |
A common pattern: offer ACH as the default on large B2B invoices to protect margin, and card for smaller or one-off payments where speed matters more than fees.
Recurring ACH on QuickBooks Invoices
For retainers, subscriptions, and payment plans, ACH is well suited to recurring billing because the per-transaction cost stays low even as volume grows. With a gateway that supports recurring ACH, Shuttle can collect scheduled bank payments and record each one against the relevant QuickBooks invoice. This removes the manual step of re-requesting payment every cycle and keeps the books matched without a reconciliation backlog.
How ACH Payments Reconcile Back into QuickBooks
The reconciliation problem is the reason most businesses avoid mixing gateways and QuickBooks: payments arrive in one system and invoices live in another, so someone has to match them by hand.
Shuttle closes that gap. When a customer pays an invoice by ACH, the QuickBooks Online Invoice Payments app marks that specific invoice as paid and records the payment against it. Whether the payment came from the invoice, a link, or a voice call, it lands in the same place. Finance sees a matched, paid invoice rather than an unallocated deposit.
QuickBooks ACH Payments FAQ
Does QuickBooks charge for ACH payments? Through QuickBooks Payments (Intuit's processor), ACH costs 1% per transaction capped at $10. If you collect ACH through your own gateway with Shuttle, you pay your gateway's ACH rate instead.
How long do ACH payments take to settle? ACH typically settles in 1 to 4 business days, slower than card but cheaper, which is why it suits larger and recurring invoices.
Can I take recurring ACH payments in QuickBooks? Yes, with a gateway that supports recurring ACH. Shuttle collects scheduled bank payments and records each against the matching QuickBooks invoice.
Is ACH on QuickBooks invoices secure? Yes. Payments run through your gateway in a PCI DSS Level 1 compliant environment, and bank details are never handled manually.
Can I collect ACH over the phone? Yes. Shuttle's Voice Checkout takes ACH bank payments on a live call and posts them back to QuickBooks, which card-only phone payment tools cannot do.
Get Started
If your gateway supports ACH, you can collect it on your QuickBooks invoices without switching processor and without manual reconciliation.
See QuickBooks payment options and connect your gateway
Add payment links to invoices: QuickBooks Payment Links
Full setup walkthrough: How to Accept Payments on QuickBooks Invoices
Collect bank payments over the phone: Voice Checkout
Questions about your gateway or pricing? Talk to us or see pricing