Keep QuickBooks for your books, replace what's behind the invoice. QuickBooks Payments charges a flat rate, roughly 2.99% on invoiced cards and 1% uncapped on ACH, regardless of what the transaction actually costs. GivePayments runs interchange-plus with Level 2/3 enhanced data on commercial cards and flat or capped ACH, and syncs everything back into QuickBooks through a full API integration or CSV import/export in QuickBooks' own format.
Answer first
For a lot of businesses, QuickBooks is the operating system: invoices go out of it, the books live in it, and when Intuit offers one-click payments on those invoices, turning it on feels obvious. That convenience is real, and for a small consumer-facing business with modest volume, it's often fine. The trap is assuming the payments product must be as good a fit as the accounting product. They're different businesses: one is software you chose, the other is a flat-rate aggregator you defaulted into.
Flat-rate pricing means every card costs you the same headline percentage, whether it's a debit card with pennies of interchange or a corporate purchasing card that qualifies for deep Level 2/3 interchange discounts, discounts a flat rate never passes to you. And 1% ACH with no cap means your biggest, best invoices carry your biggest fees: $200 on a $20,000 bank transfer that costs a specialist a flat fee to move. If you invoice other businesses, the math compounds on every single invoice. Switching the processor doesn't mean leaving QuickBooks, our integration writes settlements, fees, and refunds back into it, by API or by CSV in QuickBooks' import format.
Side by side
| QuickBooks Payments | GivePayments | |
|---|---|---|
| Model | Aggregator built into QuickBooks | Dedicated merchant account |
| Card pricing | Flat rate (~2.99% invoiced, ~3.5% keyed)* | Interchange-plus, published ranges |
| Commercial cards (B2B) | Same flat rate, no Level 2/3 pass-through | Level 2/3 enhanced data cuts interchange |
| ACH on invoices | 1% of the transfer, uncapped* | Flat or capped fee |
| Underwriting | Instant boarding, automated review later | Underwritten before boarding, decision in writing |
| Large-invoice holds | Possible when a payment trips the model | Expected volume on file from day one |
| QuickBooks reconciliation | Native | Full API integration + QuickBooks-format CSV import/export |
| Surcharging / fee pass-through | No built-in compliant program | Compliant surcharging & dual pricing configured |
| Best fit | Low-volume, consumer-facing invoicing | B2B, invoice-heavy, and commercial-card volume |
*Intuit's published pay-as-you-go rates for QuickBooks Online at the time of writing; Desktop plans differ and rates change, confirm the current schedule with Intuit. The structural comparison, flat rate vs. interchange-plus with Level 2/3, is what decides your effective cost.
The B2B math
Two line items decide what B2B invoicing really costs. First, card mix: business, corporate, and purchasing cards dominate B2B volume and qualify for significant interchange discounts when Level 2/3 data is passed, on a flat 2.99% those discounts never reach you. Second, ACH: 1% uncapped turns your largest invoices into your largest fees, while a flat or capped ACH fee costs the same whether the invoice is $2,000 or $200,000.
When to use which
You're a small, consumer-facing business with modest card volume, mostly consumer cards, small tickets, few ACH invoices. The native convenience is worth more than the interchange you're leaving on the table, and there's no reason to add a vendor for volume that doesn't justify it.
You invoice other businesses, your average ticket is meaningful, your customers pay with company cards, or you move real money over ACH. That's when flat-rate pricing and 1% uncapped bank transfers start costing four and five figures a year versus interchange-plus with Level 2/3, money that reconciles right back into the same QuickBooks file either way.
Migrating
The switch is smaller than it sounds because QuickBooks stays exactly where it is. We underwrite and board your account, you start sending invoices and pay-by-links backed by GivePayments processing, and transaction data flows back into QuickBooks two ways: a full API integration for automatic sync, or CSV import/export in QuickBooks' native format if you prefer file-based reconciliation. Works with the workflows QuickBooks Online and Desktop users already run.
Because we underwrite before boarding, your expected invoice sizes and monthly volume are part of the approval, so the $40,000 invoice that might trip an aggregator's risk model is just a Tuesday on your account. Rates are published as ranges up front, your final rate is set in a written underwriting decision, and if you want to offset card costs entirely, we configure compliant surcharging or dual pricing, something QuickBooks Payments doesn't offer built-in.
FAQ
Yes. QuickBooks the accounting software and QuickBooks Payments (Intuit merchant services) are separate products, and you can keep the first while replacing the second. Any processor that syncs its transaction data back into QuickBooks can sit behind your invoices instead of Intuit. GivePayments does this with a full API integration plus CSV import/export in QuickBooks' own format, so invoices get paid through us, and your books reconcile in QuickBooks exactly as before.
On QuickBooks Online's pay-as-you-go pricing, Intuit's published rates run roughly 2.99% for invoiced and online card payments, about 3.5% for keyed-in cards, around 2.5% for card-reader payments, and 1% for ACH bank transfers with no cap, so a $20,000 invoice paid by bank transfer costs about $200. Rates differ on QuickBooks Desktop plans and change over time, so always confirm the current schedule with Intuit. The structural point doesn't change: it's flat-rate aggregator pricing, one rate no matter what card your customer used.
Because B2B card mix skews toward commercial, corporate, and purchasing cards, and the card networks discount interchange on those cards substantially when Level 2 and Level 3 data (tax, customer code, line items, freight) is passed with the transaction. On a flat 2.99%, that discount exists, but the processor keeps it. On interchange-plus pricing with Level 2/3 enabled, the discount lands on your statement. The bigger your average invoice and the more business cards you take, the more the flat rate quietly costs you.
Yes, and thousands of businesses do exactly that. QuickBooks remains your accounting system; the processor changes behind the invoice. With GivePayments you send invoices and pay-by-links backed by our processing, and settlements, fees, and refunds flow back into QuickBooks through our API integration or a CSV export in QuickBooks' import format, whichever fits your workflow. Reconciliation stays inside QuickBooks; only the cost of acceptance changes.
GoPayment is Intuit's mobile card-acceptance app, the on-the-go arm of QuickBooks Payments, using the same merchant account and similar pricing. If you're evaluating GoPayment because your team takes payments by phone or in the field, a virtual terminal on a merchant account with interchange-plus pricing typically covers the same use case (keyed and remote payments) with Level 2/3 support that GoPayment's flat rate never passes on.
Intuit, like every aggregator, reviews transactions after boarding and can hold deposits when a payment looks unusual for your profile, a big first invoice, a spike in volume, a new business category. That's not malice, it's how minimal-upfront-underwriting models manage risk. A dedicated merchant account inverts the sequence: underwriting happens before boarding, your expected volume and ticket size are on file, and a large invoice is what your account was built for rather than a red flag.
If your invoices run through QuickBooks and your customers pay with company cards or big ACH transfers, interchange-plus with Level 2/3 is the single biggest lever on what you keep.