When an online store grows, its card bill grows at the same speed, because most checkout pricing is a percentage of every sale. A cheaper setup usually comes from one of three moves: lowering what you pay on your current checkout, using a different payment provider with the same store, or opening your own merchant account on interchange-plus pricing, where the real card costs are passed through and the markup is shown on its own line. This guide explains each move, which fee lines to check on Shopify Payments or any provider, what our 2026 pricing study found for online sales, and what to ask before you change anything.
The short answer
- There are three routes. Lower the cost where you are, use a different provider with the same store, or open your own merchant account.
- Online is where pass-through pricing showed the biggest gap. In NPS’s 2026 pricing study, a model, online and invoice sellers paid 19% to 31% less on interchange pass-through than on flat rate.
- The rate is not the whole bill. Look at fees for using another provider, currency conversion, disputes, held funds and payout timing.
- Do not assume it will plug in. Ask any provider, including us, whether it works with your store platform before you plan around it.
- Read the provider’s own pricing page. We do not quote Shopify’s current prices because they change.
Why the card bill grows with the store
A flat percentage on every online sale is easy to understand and easy to start with. A flat percentage stays the same at any volume. A store that sells $5,000 a month and a store that sells $100,000 a month pay the same rate on each dollar, so the cost rises in proportion to sales. That is fine at the start, because you have bigger problems than a fraction of a percent. It becomes a real line in the budget once the store has volume, repeat customers and a team to pay.
Online sales are also priced differently from sales at a counter. A card that is typed in or entered at checkout, with no card in the customer’s hand, is called a card-not-present sale. In NPS’s 2026 pricing study, discussed below, the model assumed higher blended credit-card interchange online than in person (2.05% plus 10 cents online, against 1.80% plus 10 cents in person). Your online store lives in the online category all day.
Before comparing anything, learn what you pay now. Your effective rate is the total of your processing fees in a month divided by your total card sales for that month. Our guide to reading your merchant statement shows how, and the same method works with a payment dashboard instead of a statement. Use three months of data rather than one, since a holiday spike or a few large orders can distort a single month.
Route one: lower the cost where you are
This is the easiest move and often the first one to try. It does not touch your checkout, so it carries no risk of breaking sales.
- Read your plan and your pricing page again. Platforms change plans and rates over time. Check whether a different plan level changes your card rate, and whether the saving beats the plan fee.
- Look for fees unrelated to the rate. Disputes, currency conversion for international orders and add-on apps can each add up.
- Cut chargebacks. Every dispute costs you a fee, the sale and your time. Clear product descriptions, clear billing names and quick replies to customers lower the number. See our chargeback survival guide.
- Ask for a review at your size. A rate set when you were small may not reflect the store you have now.
If your pricing page is the same flat percentage for everyone, this route has limits. That is when the next two routes matter.
Route two: a different payment provider on the same store
Many store platforms let you connect a payment provider other than their own. That can change the card rate without moving your product catalog or your checkout design. It can also add costs, and this is where owners get surprised.
Ask the platform, in writing, two things. First, whether it charges an extra fee when a customer pays through another provider, and how much. Second, which features you lose, such as a built-in payout report, a saved-card wallet or a one-click checkout. If the platform fee for using an outside provider is about the same as the saving you were hoping for, route two does not help you.
Then ask the provider you are considering how it connects to your platform. Some connect with a plugin, some with a hosted payment page, and some with an API, which is a set of instructions that lets two programs talk to each other. NPS offers a gateway with API and webhook options and a free WooCommerce plugin, and we explain the pieces in online credit card acceptance: a merchant’s complete guide. Whether a given provider works smoothly with your particular store platform is a factual question, not an assumption. Ask us, or any provider, before you plan a switch around it.
Provider Connection
How a provider can connect to your store
| Connection method | How it works | NPS availability |
|---|---|---|
| Plugin | Installs into your store platform | Free WooCommerce plugin |
| Hosted payment page | Customer sent to provider’s page to pay | Ask provider to confirm |
| API | Set of instructions that lets two programs talk to each other | Gateway with API and webhook options |
Route three: your own merchant account on interchange-plus
A merchant account is the account that receives your card payments before they are sent to your bank. Some providers give each business its own. Others group many businesses under one master account, which is called a payment aggregator model. Ask any provider which one you would be on, because it affects how risk is judged and who can pause your funds.
On a merchant account you can choose interchange-plus pricing, also called pass-through or cost-plus. The real fees from the card-issuing banks and the card networks are passed through at cost, and the provider adds a markup that is stated on its own line. Debit costs less than a premium rewards card, and your statement shows both. NPS publishes no rates, because pricing depends on your volume, ticket size and card mix. Our guide to the four merchant account pricing models compares flat rate, tiered, interchange-plus and membership pricing, and where payment fees actually go explains the layers.
The tradeoff is effort. Statements are longer, and opening a merchant account involves a review of your business. Ask each provider what documents it needs and how long approval takes. A provider that tells you it is a merchant account should tell you what documents it needs.
What our 2026 pricing study found about online sales
NPS published a pricing study in 2026 that compares flat-rate pricing with interchange pass-through pricing. Two cautions come first. It is a model built on published rate schedules, not a survey of real stores, and it was written by a processor that sells pass-through pricing. It did not model Shopify Payments.
In the model, businesses selling online or by invoice paid 19% to 31% less on pass-through than on flat rate, across average tickets from $15 to $2,500. The study’s online flat-rate benchmark was the 2.9% plus 30 cents rate that Stripe published for online card payments in October 2026. That is a benchmark for the comparison, not a statement about what you pay.
In the study, the biggest gap shows up on debit cards and invoices. Federal rules cap the fee on debit cards issued by large banks at 0.05% of the sale plus 21 cents, with a 1 cent fraud adjustment. Debit cards from smaller banks are exempt and cost more, and the study assumed that 35% of debit volume came from exempt cards. It also assumed that debit made up about 35% of card sales on a $40 order, 30% on a $75 order and 25% on a $150 order. Those mix numbers came from NPS merchant experience and are inputs, not measurements of your store.
2026 Pricing Study
Flat rate vs. interchange pass-through online
- What online sellers paid in the model
- Flat rateBenchmark: 2.9% plus 30 cents
- Interchange pass-through19% to 31% less than flat rate
- How the markup is shown
- Flat rateOne blended percentage on every sale
- Interchange pass-throughProvider markup stated on its own line
- Debit card cost
- Flat rateSame flat rate as credit
- Interchange pass-throughFederal rules cap large-bank debit at 0.05% plus 21 cents
- Statement complexity
- Flat rateSimple, one rate
- Interchange pass-throughLonger; real card costs shown separately
Online and invoice sellers paid 19% to 31% less on interchange pass-through than on flat rate.
Notice what that means for you. If your customers are mostly young or your orders are small, you may have more debit and the model’s gap may be larger. If your orders are large and paid on business cards, interchange is higher and the gap narrows. The only way to know is to price your own transactions. The study makes no promise for your store, and neither do we.
The fee lines to look for on Shopify Payments, or any provider
Open Shopify’s current pricing page and your latest payout report, and write down each of these. Do the same for every quote you collect.
- Online card rate. The percentage and the fixed amount per order.
- In-person rate. This matters if you also sell at pop-ups or a store.
- Fee for using another provider. Whether the platform adds a charge when you do not use its own checkout payments, and how much.
- Currency and international fees. Charges for converting currency or accepting cards from other countries.
- Dispute fees. What a chargeback costs, and whether it is returned if you win.
- Payout timing. How many days until the money reaches your bank, and what an early payout costs.
- Holds and reserves. When can funds be held back, for how long, and what you can do about it.
- Monthly and plan fees. Platform subscription, gateway, PCI compliance and statement charges.
- Contract terms. Length, renewal and early termination.
Fee Audit
Fee lines to check on any provider
- Check the online card rate: the percentage and the fixed amount per order
- Check the fee for using another provider on your platform
- Check currency and international fees for orders from other countries
- Check dispute fees and whether the fee is returned if you win
- Check payout timing and what an early payout costs
- Check holds and reserves: when funds can be held and for how long
That list works for Stripe, Square, PayPal and others as well. If a line is missing from the provider’s pricing page, ask them to put it in writing. For a longer list of questions, see 20 critical questions to ask your payment processor before signing.
Cost is not the only reason stores move
A lower rate matters, but it is rarely the only reason an owner starts asking about alternatives. Three others come up again and again.
Held funds and account reviews. When you are paid before your orders ship, or you sell items that attract disputes, a provider may review your account or hold funds. Ask each provider how reviews work, who you speak to, and how long a typical review takes. NPS describes the difference between a pooled account and your own merchant account in Stripe alternative for small business.
Support. A large self-service platform may route you to help articles and chat. Ask whether you can phone a person, and ask for the number before you sign. Judge that for yourself by calling and timing it. We discuss why this matters in transparent payment processing plus real support.
Control of the data. If your payments live inside your store platform, moving the store later also means moving your payment setup. A provider you control separately makes the store easier to change.
Disputes and fraud tools for online stores
An online store sees more disputes than a shop, because the buyer and the card are never in the same room. Ask each provider what dispute tools come with the account. NPS’s statement guide says e-commerce merchants should be enrolled in a chargeback program so they can use tools such as RDR, Ethoca and CDRN. These are chargeback programs. Ask a provider whether any of them are included, what they cost, and which kinds of disputes they cover.
For the disputes you cannot avoid, keep records. Order confirmations, shipping tracking, delivery signatures and customer messages all help. Our guide on how to prevent and win disputes walks through what to keep.
A simple way to compare, using your own numbers
Here is an example with made-up numbers, to show the arithmetic. Say your store processes $30,000 a month in card sales and your fees are $990. Your effective rate is 3.3%, because $990 divided by $30,000 is 0.033. A quote that comes in at an effective rate of 2.8% would cost $840, which is $150 less a month, or $1,800 a year. That is a hypothetical, not a promise. Your own volume, card mix and order sizes will give you different numbers.
To do this with real data, download about 90 days of orders and fees from your dashboard. Then ask each provider to price the same 90 days of transactions, not an average, and to show you the result line by line. NPS explains the steps in how much are you really paying Stripe, Square, PayPal or QuickBooks, and our statement review is free.
Common mistakes when looking for cheaper checkout fees
- Comparing a headline rate to an effective rate. Compare the same thing on both sides.
- Forgetting the platform fee for using an outside provider.
- Switching in the middle of your busiest season. Plan the change for a slow week, and test it with a real order before you announce anything.
- Leaving no way back. Keep your old payment setup active until the new one has processed real orders and paid out to your bank.
- Believing a saving that has no stated inputs. A good quote says what card mix and order size it assumed.
For the full picture across every sales channel and average ticket, read our guide to cheapest payment processing in 2026.
Beyond Shopify Payments, our guide to the best payment processors compares ten other providers by business type.
Who wrote this, and where NPS fits
Nationwide Payment Systems (NPS) publishes this guide. We are a payments company, in business since 2001, and we sell merchant accounts, a payment gateway, invoicing and point of sale systems, so we are not neutral. We offer interchange-plus (cost-plus) and simplified pricing, and we do not publish one universal rate. You can read more in our guide to taking payments online, browse the payments guides, or contact our team for a second opinion on a quote.
We are not the right fit for everyone. If you are a new store with very low volume and want the simplest start, the checkout your platform provides may serve you well for now. We do not quote competitors’ current prices, because those change. Read each provider’s own pricing page.
Bottom line
Cheaper card costs for a growing online store come from three moves: lower the cost where you are, use a different provider, or open a merchant account on interchange-plus pricing. In NPS’s 2026 pricing study, a model, online sales showed the biggest gap between flat rate and pass-through, but your own card mix decides your result. Check the fee for using another provider, disputes, payout timing and held funds, and ask whether a provider works with your store before you plan around it. Read Shopify’s own current pricing page, price your last 90 days, and compare line by line. If you want a second opinion, contact our team, and if staying put is the better answer, we will say so.
Frequently asked questions
What are cheaper alternatives to Shopify Payments?
There are three routes. Lower your cost on your current checkout, connect a different payment provider to the same store, or open your own merchant account on interchange-plus pricing. Each has tradeoffs, so list every fee line first and compare real numbers.
Does using a different payment provider cost extra on my store platform?
It can. Some platforms charge an additional fee when customers pay through an outside provider. Ask the platform in writing what the fee is, and subtract it from any saving before you decide. We do not quote current platform prices.
What is interchange-plus pricing for an online store?
It is pricing where the real fees from card-issuing banks and networks are passed through at cost, and the provider adds a markup on its own line. It is also called pass-through or cost-plus pricing. In NPS’s 2026 pricing study, a model, online sellers paid 19% to 31% less on it than on flat rate.
Will a merchant account work with my store platform?
Not every provider connects to every platform. Ask whether it connects by plugin, hosted page or API, and ask for confirmation before you plan around it. NPS offers a gateway with API and webhook options and a free WooCommerce plugin, and you should ask us about your specific platform.
Why do online stores see more disputes?
The customer and the card are never in the same place, so it is easier for fraud and for honest mistakes. Ask providers about dispute programs such as RDR, Ethoca and CDRN, and keep order, shipping and customer records for every sale.
How do I find out how much I really pay?
Divide your total processing fees by your total card sales for the same period to get your effective rate. Use about 90 days of data. NPS offers a free statement review, with no obligation to switch.
