Written by Robert Day, Founder and Managing Partner of weAudit.com, who spent more than a decade as an executive at Fifth Third Processing Solutions, later Vantiv and Worldpay, now part of Global Payments. Published October 2026.
The short version
Integrated payments let you take cards inside the software you already run your business on. That convenience is real.
So is the second revenue stream behind it. Your software company is commonly paid on every card you process, either as a share of the processing fees or as a markup it sets itself.
That does not make integrated payments a bad choice. It means the rate inside your software deserves the same scrutiny as any other processing contract.
Integrated payments are card and ACH payments taken directly inside a business software platform, such as an accounting system, an ERP, a field service app, or a booking system, instead of through a separate terminal or a separate processor’s website. The payment posts to the invoice automatically, so nobody has to key it in twice or reconcile it by hand.
You will see the same idea sold as embedded payments, built-in payments, or “get paid faster” inside your software. Underneath every version sits an ordinary card processor. The software company has simply placed itself between you and that processor.
That placement is the part most businesses never see, and it is where the cost question lives.
This section comes straight from Stripe’s own sales material. Stripe publishes a guide called “How to choose a monetization strategy for your SaaS platform,” and its audience is not merchants. It is written for software companies, to persuade them to build Stripe into their product and earn a cut of every card their customers run. In other words, it is a recruiting pitch for the people who sell you your software. It lays out two ways they get paid. Both are standard across the industry, not unique to Stripe.
You pay the processor’s standard rate, in Stripe’s case 2.9% plus 30 cents per card transaction. The processor then passes a portion of what it earned from you back to your software company. You see one fee. You do not see the split.
The software company pays the processor its cost, then sets whatever price it chooses to charge you and keeps the difference. Stripe’s guide presents this as giving the platform more control over pricing, including tiered pricing and custom pricing for individual users. In plain terms, two businesses on the same software can pay very different rates.
$900,000
The annual headcount cost Stripe’s own guide estimates for a software company to run a buy-rate payments business properly, across product, sales, legal, risk and finance. Nobody spends that to break even on payments. Processing is a profit line for the software companies that build it.
Stripe is not warning merchants about any of this. It is selling it to the companies merchants trust to run their business.
Card processing is a non-regulated industry. No rule requires your software vendor to tell you which model it uses, how much it keeps, or how its rate compares to what you could get elsewhere.
The trade is convenience against control. Here is how the two usually compare.
The software subscription is not where the money goes. The processing rate is. Most of what a card transaction costs is interchange, the fee set by Visa and Mastercard that every processor pays. Visa and Mastercard now price domestic credit cards across 640 interchange categories, and the processor’s markup is everything on top.
A flat integrated rate folds interchange and markup into one number, so you cannot see the markup at all. Here is what that gap looks like at $1 million a year in card volume, using illustrative figures.
| Pricing | Rate | Yearly cost |
|---|---|---|
| Typical flat integrated rate | 2.90% | $29,000 |
| Interchange plus 5 basis points | 2.30% | $23,000 |
| Difference | 0.60% | $6,000 |
Illustration only. 2.25% is the typical blended interchange weAudit sees in its audits; your mix will differ. The flat rate excludes the per-transaction fee, which widens the gap further.
For B2B companies the gap is often wider. Business and purchasing cards qualify for lower interchange when the payment carries Level 2 and Level 3 data, such as tax amount, purchase order number and line items. On a flat rate, the processor collects that saving and you keep paying the same number. A low quoted rate is also not the same as a low cost, since fees can be added or invented outside the rate itself.
Often, yes. Most businesses on QuickBooks, Sage, NetSuite, Acumatica, Microsoft Dynamics or Prophet 21 assume the card fees are fixed by their software. In most cases they are not. Many platforms let you connect your own processor, and many let you choose your own gateway.
The gateway matters more than most people expect, because it controls whether your transactions carry the data that qualifies them for the lowest interchange, and interchange is roughly 90% of total processing cost. Getting a better processor is important. Getting a better gateway is very important.
If you are on QuickBooks Payments specifically, our QuickBooks Payments fees page breaks down every current rate. For platforms built on Stripe, see Stripe fees.
Before you turn integrated payments on, or the next time your rate comes up, ask these in writing.
1. Do you earn anything when we process a card? Revenue share, markup or residual, any of them counts.
2. Is our rate flat, tiered, or interchange plus? Only interchange plus shows you what the processor is actually keeping.
3. Does the integration send Level 2 and Level 3 data? If you take business cards and the answer is no, you are likely paying more interchange than you need to.
4. Can we connect our own processor or gateway? If not, the processing rate is part of your software contract and should be negotiated with it.
5. Can you change our rate without notice? Merchant agreements commonly allow fee changes at any time, so a signed rate is a starting position, not a guarantee.
Integrated payments are card and ACH payments accepted directly inside business software, such as an accounting system, ERP or booking app, so each payment posts to its invoice automatically. A card processor still handles the transaction behind the scenes.
Often, yes. Software platforms commonly earn either a share of the processing fees you pay or a markup they set on top of the processor’s cost. Ask your vendor directly which applies to you.
Not always, but flat integrated rates often cost more than properly priced interchange plus, because the markup is hidden inside one number. At $1 million a year, a 0.60% difference is $6,000.
The terms overlap. Embedded payments usually means the software company itself sells and controls the payment service, while integrated payments can also mean connecting an outside processor to your software. For the business paying the fees, the cost questions are the same.
In many cases, yes. Platforms such as QuickBooks, NetSuite, Acumatica, Microsoft Dynamics and Prophet 21 often allow an outside processor or gateway. Check your software agreement and ask the vendor which processors and gateways it supports.
Divide your total monthly processing fees by your total card volume to get your effective rate, then compare it to roughly 2.25% plus a few basis points. A free statement audit will show exactly where the difference goes.
weAudit takes no revenue share, no referral arrangement and has no financial tie to any processor or ISO. The first audit is free.
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In 2009 the US Government Accountability Office counted the interchange rate categories Visa and Mastercard used to price credit card transactions. It found 303. Nobody has updated that count since. We did.
