One option for an ecommerce store that wants to take payments instead of Shopify Payments or Stripe is a merchant account on interchange-plus pricing (where you pay the real card cost plus a disclosed markup) connected to your store through a payment gateway. In NPS’s study, a model finds pass-through pricing costs less than flat rate online, and the dollar gap grows with the ticket while the percentage gap narrows (from 31% at a $40 ticket to 23% at $2,500 in the study’s online inputs). It may not save money for a brand-new store with very few orders, and your platform may charge extra or limit your options if you use an outside provider, so check that first. This guide explains where online savings come from, what the study says, which fees to compare and when to stay where you are.
The short answer
- Online is where the study finds the largest gap. In NPS’s 2026 pricing study, a model finds online and invoice sellers paying 19% to 31% less on pass-through pricing across tickets from $15 to $2,500.
- The study is a model from a processor that sells pass-through pricing, so test it on your own orders.
- Stripe’s online price is 2.9% plus 30 cents per the study (accessed October 2026). For Shopify Payments and others, read the provider’s current pricing page.
- Your platform matters. Ask whether it lets you use an outside provider and whether it adds a fee if you do.
- Flat rate can be cheaper for a very new store with very low volume.
What you pay now, and what is inside it
Every online card sale carries three costs: the interchange fee paid to the bank that issued the shopper’s card, the card networks’ own assessment fees, and the markup charged by whoever processes the payment. A flat-rate provider charges one number for all three. NPS’s 2026 pricing study uses Stripe’s published online price of 2.9% plus 30 cents as its online flat-rate benchmark, accessed October 2026.
A little arithmetic shows what that means for a store. A $75 order costs about $2.48 in fees at that price, and a $150 order costs $4.65. A store with 1,000 orders of $100 in a month ($100,000 in sales) pays $2,900 in percentage fees plus $300 in per-order fees, or $3,200 in all, before refunds, disputes, currency conversion, payout fees and any platform fee. That is arithmetic on the quoted price, not a prediction of your bill.
Flat-Rate Benchmark
What Stripe charges for online payments
- Per transaction2.9% + 30¢Stripe online card paymentStudy quotes Stripe’s published online price, accessed October 2026. Read Stripe’s current pricing page for any changes.
- Example: $100 order × 1,000$3,200One month at $100,000 in sales$2,900 in percentage fees plus $300 in per-order fees, before refunds, disputes, currency conversion, payout fees and any platform fee.
We do not quote Shopify Payments’ price here. It changes by plan, country and card type, and you should read the provider’s current pricing page and your own plan’s terms. Look for: the online card rate, a fixed fee per order, any rate for international or foreign-currency cards, the cost of a dispute, payout fees, and any extra charge for using an outside payment provider.
Why online sales are where interchange plus can help most
Interchange plus separates the three costs. You pay what the card networks charge for each card, plus one markup stated in your agreement. NPS explains the model and the other main pricing models in its guide to merchant account pricing models.
The study is “The Flat-Rate Tax,” by Allen Kopelman, the CEO of NPS. It is a cost model built on published rate schedules, not a survey, and it was written by a processor that sells pass-through pricing. It says businesses selling online or by invoice pay 19% to 31% less in processing costs on pass-through than on flat rate, across average tickets from $15 to $2,500. Link: NPS’s 2026 pricing study.
Two features of the model explain the online result. First, debit cards. Under federal rules (the Durbin Amendment, put into effect as Regulation II), interchange on debit cards from large banks is capped at 0.05% of the sale plus 21 cents, with a 1 cent fraud adjustment, and a flat rate charges the full percentage anyway. Second, the gap between a flat online price and the true cost of the average card is wider online than in person in the model’s assumptions.
Debit cards and order size
Be careful with the word “most.” The cap covers debit cards from large banks. Debit cards from smaller banks are exempt and cost more. In the study’s model, 35% of debit volume is assumed to come from exempt issuers. The Federal Reserve has also proposed lowering the cap, and the study calls that proposal unresolved.
How much debit your shoppers use depends on what you sell and to whom. The study says debit makes up roughly 30% to 40% of card payments on sales under $100 and about 20% to 25% over $100. Its model uses 35% at a $40 ticket, 30% at $75, 25% at $150, 22% at $300 and 15% at $1,000. Those figures come from NPS merchant experience and are model inputs. Younger shoppers use debit more, and luxury and big-ticket purchases lean toward credit.
Debit Card Mix
Debit share drops as ticket size rises
| Average ticket | Debit share (model) | Credit lean |
|---|---|---|
| $40 | 35% | Younger shoppers, lower-cost goods |
| $75 | 30% | Mixed card use |
| $150 | 25% | Shifting toward credit |
| $300 | 22% | Mostly credit |
| $1,000 | 15% | Luxury and big-ticket purchases |
A store selling $30 accessories to younger shoppers will probably have more debit than a store selling $600 furniture. Ask your current provider for a report of orders by card type, or run a sample of orders through a card-type lookup if your dashboard shows it. Then you will know whether the debit effect matters for you.
Your platform comes first
Before you compare rates, find out what your store platform allows. The answers decide whether the cheapest option is available to you at all. Ask or read the platform’s own terms for these points:
- Can I use a payment provider other than the platform’s own?
- If I do, does the platform charge an extra fee on each order, and how much?
- Which gateways and payment apps are supported, and does my checkout keep wallets such as Apple Pay and Google Pay?
- Do payouts, refunds, disputes and reporting work the same way?
- What happens to my saved cards and subscriptions if I change providers?
This is a question about your platform’s rules, and the answers can change, so get them from the platform in writing. NPS says it offers a free WooCommerce plugin for stores on WordPress, a payment gateway with a developer API and webhooks, payment links, a virtual terminal and Apple Pay and Google Pay, plus integrations with leading shopping carts. See the guide to taking payments online. Ask NPS or any provider which carts it supports before you assume yours is covered.
Platform Check
Ask your platform before switching providers
- Ask whether outside payment providers are allowed
- Ask whether the platform charges an extra fee per order for using one
- Ask which gateways and payment apps are supported
- Ask whether checkout keeps wallets such as Apple Pay and Google Pay
- Ask what happens to saved cards and subscriptions if you change providers
- Get the platform’s answers in writing
Account holds and reserves
Cost is not the only reason stores look for another provider. Ask any provider, including your current one, whether it keeps a reserve, how long payouts take, and what you can do if a payout is held. See the guide to a Stripe alternative for small business.
A dedicated merchant account is one that is underwritten for your business alone. NPS describes that as a benefit, and it comes with underwriting. You will be asked about your business, your products, your refund policy and your processing history. Ask any provider how long approval takes, what reserve or hold policies apply, and what you can do if a payout is held.
If your products are in a category some providers treat as higher risk, say so up front. Some stores move because one provider declined or froze them. NPS has a survival guide for that situation, Stripe shut me down: a high-risk or startup merchant survival guide, and a Q&A on credit card processing companies for small business that lists what to compare.
When Shopify Payments or Stripe is still the cheaper choice
The study says plainly that flat rate is sometimes the better deal. Its examples are in-person businesses with very small tickets, around $15 and under, and brand-new businesses with very low volume. For a new online store with a handful of orders a week, a flat rate with no monthly fee, no contract and no application is hard to beat. It also lets you test products before you commit to a bigger setup.
NPS’s pricing guide says the same thing in dollars: flat rate is best for startups and merchants processing under $10,000 a month, and interchange plus is best for businesses processing over $25,000 a month. A store somewhere between those numbers should price both.
Pricing Models
Flat rate vs. interchange plus for online stores
- Who is it best for?
- Flat rateStartups, under ~$10,000 a month
- Interchange plusBusinesses over $25,000 a month
- What do you pay?
- Flat rateOne number covers all three costs
- Interchange plusReal card cost plus one disclosed markup
- Debit card savings?
- Flat rateFull percentage charged anyway
- Interchange plusCapped rate passed through on large-bank debit
- Setup friction?
- Flat rateNo contract, no application
- Interchange plusUnderwriting required for your business
For an ecommerce store with steady sales, interchange plus through your own merchant account is the option to price against Shopify Payments or Stripe, if your platform allows it without a penalty.
The other reason to stay is that built-in payments are convenient. When payments, payouts, taxes, fraud tools and reporting live in the platform, you spend less time on setup. If an outside provider adds a platform fee on every order, that fee can cancel out much of the savings. That is why the platform check above comes first.
What else to compare besides the rate
Fees that sit outside the rate can decide the winner. Put each one next to the same month of orders:
- Monthly, gateway, PCI, statement and software fees.
- Dispute fees. The study notes Stripe’s $15 per dispute plus $15 to respond manually, refunded if you win. Compare with what any provider charges.
- Fees on international cards and currency conversion.
- Fees for manually keyed orders. The study quotes an extra 0.5% on Stripe for manually entered cards.
- Payout speed and any fee for instant payouts.
- Contract length, early termination fees and hardware leases, if any.
Add chargeback handling to the list. An online store sees disputes, and the way a provider helps you respond affects how much you lose. NPS has a guide on chargebacks for ecommerce and describes fraud detection, tokenization and encryption in its gateway. Ask any provider what tools come with the account and what costs extra.
How to get a fair quote
Pull the last three months of orders from your platform and your payment provider: number of orders, total sales, average order, refunds, disputes, total fees and the share of international cards. NPS says its statement review is free. See how much you are really paying on Stripe, Square, PayPal or QuickBooks.
Ask each provider to price that exact period in dollars, all fees included, and to say what platform fee, if any, your store would add. Then compare the effective rate (total fees divided by total sales) and the dollars a year. A saving that disappears once the platform’s fee is counted was never a saving.
If a provider will not do the math on your own orders, or will not state the markup in writing, treat that as information.
One last habit worth building: repeat the comparison once a year. Your order size, card mix and volume change, and so do the published prices of every provider. A store that was right to stay on a flat rate at $5,000 a month may be paying a premium at $50,000 a month, and a store that switched may find its needs have changed again. Write down your effective rate each quarter, and a jump will show you when it is time to ask for a new quote.
Getting a Fair Quote
How to compare your real processing cost
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Pull three months of ordersPull the last three months of orders from your platform and your payment provider: number of orders, total sales, average order, refunds, disputes, total fees and the share of international cards.
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Check your platform’s rulesAsk whether it lets you use an outside provider and whether it adds a fee if you do.
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Ask for a dollar quoteAsk each provider to price that exact period in dollars, all fees included, and to say what platform fee, if any, your store would add.
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Compare effective rateCompare the effective rate (total fees divided by total sales) and the dollars a year.
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Repeat once a yearYour order size, card mix and volume change, and so do the published prices of every provider.
Keep the same three numbers each time: total sales, total fees and number of orders. With only those, you can compute your effective rate and your cost per order in a few minutes, and compare any new quote against them without relying on anyone’s headline.
For the full picture across every sales channel and average ticket, read our guide to cheapest payment processing in 2026.
Who wrote this, and where NPS fits
Nationwide Payment Systems (NPS) publishes this guide. We are a payments company based in Fort Lauderdale, Florida, in business since 2001, and we sell merchant accounts and a payment gateway, so we are not neutral. We offer interchange-plus pricing, a gateway with a developer API, payment links and a free WooCommerce plugin, and we also offer flat-rate options. We do not publish a price list, because pricing depends on volume, order size, card mix and risk. The study we cite was written by our CEO. Browse more in our payments guides or see where Stripe fees actually go.
We are not the right fit for every store. If you are just launching, want to take your first order today, or your platform charges an extra fee for outside providers, your current setup may cost you less.
Bottom line
For an ecommerce store with steady sales, interchange plus through your own merchant account is the option to price against Shopify Payments or Stripe, if your platform allows it without a penalty. In NPS’s study, a model finds the largest savings of any channel online and by invoice, and it also says flat rate can win for very small or very new operations. Check your platform’s rules first, compare every fee and ask for a quote built from your last three months of orders. If you would like a second opinion on a quote or on your current statement, you can contact our team, and if staying where you are is the better answer, we will say so.
Frequently asked questions
Is there a cheaper way to take card payments online than Stripe?
Often, for stores with steady sales. In NPS’s 2026 pricing study, a model finds online sellers paying 19% to 31% less on pass-through pricing than on flat rate, across tickets from $15 to $2,500. It is a model from a processor that sells pass-through pricing, so test it on your own orders.
What does Stripe charge for online payments?
The study quotes Stripe’s published online price as 2.9% plus 30 cents per card payment, accessed October 2026. Read Stripe’s current pricing page for any changes.
Does my store platform allow another payment provider?
That depends on your platform. Ask it whether outside providers are allowed, whether it charges an extra fee per order for using one, and which gateways it supports.
Why do debit cards matter for online stores?
Debit cards from large banks are capped by federal rules at 0.05% plus 21 cents, with a 1 cent fraud adjustment, while a flat rate charges the full percentage. The cap does not cover debit cards from smaller banks, which cost more.
When is a flat rate the better deal for an online store?
The study says it can be for brand-new businesses with very low volume. NPS’s pricing guide lists flat rate as best for merchants under about $10,000 a month.
Does NPS work with WooCommerce?
NPS says it offers a free WooCommerce plugin for WordPress stores, plus a gateway, payment links and integrations with leading shopping carts. Ask which cart you use.
Does NPS review my current statement for free?
Yes. NPS offers a free statement review. Send a recent statement and ask for the math on your own orders.
