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The Best eCommerce Merchant Services & 4 Essential Features For An eCommerce Merchant Account

Learn about the services you'll need to launch an eCommerce business, including payment services, merchant accounts, shopping carts, payment gateways, and shipping.

    Chris Motola

Advertiser Disclosure: Our unbiased reviews and content are supported in part by affiliate partnerships, and we adhere to strict guidelines to preserve editorial integrity.

The ability to buy and sell on the internet has only been available for only a few decades. In that time, however, the eCommerce industry has expanded dramatically, disrupting traditional retail industries and opening up a new world of opportunity for both merchants and consumers alike. Consumers are no longer limited to buying only things that are available in their local areas. Merchants, on the other hand, can expand their customer base from just the people living nearby to practically the entire planet.

Whether you’re looking to start an eCommerce-only business or add an online presence to your existing retail operation, there are several things you’re going to need before you can ring up your first sale. The most important thing you’ll need right away is a means for your customers to pay for their purchases. Unlike retail merchants, who can always accept cash or paper checks, you probably need to be able to accept credit and debit cards (or failing that, ACH or digital wallet payments). Traditionally, the only way to accept these types of payments was through a merchant account, which is simply an account that processes your customers’ payments and transfers the funds to you, the merchant.

Today, however, you also have the choice of using a payment service provider (PSP), which performs the same basic functions as a merchant account but doesn’t come with a bewildering assortment of fees and complicated processing rates.

Square and PayPal are popular examples of payment services providers.

This article briefly discusses the services you’ll need to launch an eCommerce business, including online shopping carts, payment gateways, and shipping services (for sellers of physical goods). Then, we’ll discuss merchant accounts in-depth, including the features you’ll want to look for and how much you can expect to pay for them. We’ll also recommend several of our highest-rated providers that are ideal for a web-based business.

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Best for eCommerce businesses that also do face-to-face transactions.
Best for eCommerce businesses that also do face-to-face transactions.

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Stripe Payments

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Best for tech-savvy eCommerce businesses.
Best for tech-savvy eCommerce businesses.

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Best for high-risk businesses.
Best for high-risk businesses.

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Read more below to learn why we chose these options.

What Is An eCommerce Merchant Account?

An eCommerce merchant account is a merchant account specifically geared toward online sellers. The merchant services provider should offer tools and integrations to make online transactions easy and safe for both customers and eCommerce merchants. This includes payment gateways, security measures, and web dashboards.

But what is an eCommerce merchant to begin with?

The term “eCommerce merchant” is a fairly common one, used broadly to refer to any type of business that sells goods or services online. This might include any of the following:

  • Traditional retailers with an online focus (clothing, shoes, accessories, etc.)
  • Artists, artisans, and crafters with handmade or limited-run goods
  • Subscription box businesses
  • Digital creators (musicians, actors, & other content creators)
  • Software-as-a-Services (SaaS) providers

The key point is that these businesses sell primarily, if not exclusively, via the internet. And as such, their needs for payment processsing are more specialized.

“eCommerce merchant services” can generally mean any payment processor that offers the ability to accept payments online.

However, most eCommerce merchants will be better off looking at services that offer more toolsets and services that are optimized for online sales. It’s important to understand that “merchant services” is an umbrella term that encompasses payment processing, reporting, business software, and sometimes even merchant cash advances. Not all payment processors or merchant services providers offer true merchant accounts — some instead fall under the category of “payment service provider” (PSP) or “third party payment processor.” For the purposes of this article, we’re talking about both traditional merchant accounts and third-party processors that can accommodate eCommerce.

Why Do You Need An eCommerce Merchant Account?

So seeing as there’s nothing special about the merchant accounts (or aggregated merchant accounts) that accept eCommerce transactions, why do you need eCommerce merchant services?

For starters, you probably don’t need all the brick and mortar POS hardware and infrastructure offered by traditional merchant services. You will, on the other hand, generally want the specialized tools and features eCommerce merchant services offer online sellers. Because having an online presence is all but mandatory for businesses these days, almost all merchant services offer both. However, each provider tends to focus more on one than the other.

If an eCommerce merchant services provider offers any services for in-person credit card processing, they are usually quite limited. Likewise, if you opt for a general merchant account, you’ll have most of the basic tools to sell online and in-person, but you’ll likely miss out on advanced technical features that allow you more power and control over your eCommerce shop.

The 3 Best eCommerce Merchant Services For Online Businesses

The best eCommerce merchant account services for online businesses combine excellent shopping cart tools, payment gateways, and security features to make online transactions simple and easy. Here are four of the best providers of eCommerce merchant accounts, including Square, Stripe, and Payment Cloud.

1. Square


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Best for eCommerce businesses that also do face-to-face transactions.


  • Comprehensive feature set
  • Predictable flat-rate pricing
  • No mandatory monthly fees
  • Free online store/website
  • Excellent brick and mortar support


  • Account stability issues
  • May not be suited for high transaction volumes
  • Limited international sales support

Square, one of the leading third-party processors in the business, began as a convenient POS system for brick and mortar businesses. That's still where its strengths lie: you'll find Square offers quality hardware and expansive support software for small businesses. Over time, however, Square has come to offer quality eCommerce support and infrastructure that includes a free online store and shopping cart support. If your sales are made up of a mix online and offline transactions, Square can be a great way to do both with minimal fuss.

Square uses a flat-rate pricing model for all of its transactions. For eCommerce transactions and invoices, Square charges 2.9% + $0.30, which is more or less the standard industry flat-rate fee for online payments. Square gives you a lot for “free,” including its classic magstripe card reader for mobile devices, a payment gateway, and a virtual terminal, but monthly fees are required for some of the meatier software.

Square is a great all-in-one solution for businesses that do a relatively low volume of transactions.

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2. Stripe

Stripe Payments

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Best for tech-savvy eCommerce businesses.


  • Excellent developer tools
  • Predictable flat-rate pricing
  • Advanced reporting, marketplace, and subscription tools
  • Able to handle multiple currencies and international sales


  • Account stability issues
  • Needs technically skill to fully take advantage of platform
  • Gateway cannot be used independently

Stripe has made a lot of effort to position itself as the Square of eCommerce. With a similar focus on being a one-stop-shop for its customers--as well as a third-party processor--Stripe mostly lives up to the comparison. However, where Square is easy to use, Stripe focuses on giving developers tools to make it easy to customize.

Stripe is open to merchants worldwide with numerous currency options and support for many alternative payment methods and local payment options across North America, the EU, and Asia. You’ll also find a great selection of marketplace tools and recurring billing options. Stripe gives you a gateway, a hosted payment page, PCI compliance, and the ability to migrate your customer data if you ever decide to leave.

Stripe charges a flat 2.90% + $0.30 per transaction. There’s no monthly fee, no monthly minimum, and no PCI compliance fee. Stripe also offers ACH payments at 0.8% that are capped at $5 per month for ACH debit and $1 per ACH credit payment. Stripe's more advanced features tend to come at an increased cost per transaction, so make sure you're getting a good return on your investment before you tack on too many optional features.

Get Started With Stripe Payments

Read our in-depth review

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3. PaymentCloud


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Best for high-risk businesses.


  • Reasonable rates and fees
  • Free credit card terminal and shopping cart integration
  • Excellent customer support
  • Flexible with payment gateways


  • No publicly disclosed pricing
  • You’ll likely need to sign a long-term contract

Businesses that deal in products or services that are considered high-risk (think anything that could fall under the category of "vice") will find that they have far fewer options available to them as far as payment processors go. Nevertheless, that doesn't mean you should accept just any service. PaymentCloud is a good example of what you should look for in a high-risk payment processor.

PaymentCloud doesn't skimp on eCommerce support, coming with shopping cart integration, ACH processing, and the ability to use any compatible payment gateway that you want.

As is usually the case for high-risk payment services, we don’t have access to pricing information in advance. That’s because companies such as PaymentCloud shop your profile around to various back-end processors to get you the best deal that they can. Typically, this means tiered-pricing, monthly minimums, and contracts (at least initially), but you can expect to be treated fairly by PaymentCloud.

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4 Must-Haves For Any Commerce Merchant Account

There are some essential eCommerce-related features you’ll want in a payment processor.

Online Shopping Carts

An online shopping cart is simply a service that integrates with your website and allows you to display products to your customers. Shopping cart software allows your customers to learn more about your products, select from different options (i.e., color choices, clothing sizes, etc.), and choose the quantity of each product they’d like to buy. Carts also perform a number of other functions to make your customers’ online shopping experience as smooth and seamless as possible.

Of course, you’ll want to select a shopping cart that integrates seamlessly with your chosen payment gateway. Both your shopping cart and your gateway must also, in turn, integrate with your merchant account. As long as you stick to a well-known shopping cart, you shouldn’t have any problems. Nonetheless, you should definitely confirm that your chosen cart is compatible with the other elements of your system before you commit to using it.

Payment Gateways

Payment gateways cause a lot of confusion because brick and mortar merchants don’t require them, but they’re absolutely necessary for eCommerce. More confusingly, sometimes payment gateways are integrated into a service (as in the case of Stripe) while other times they’re a standalone service that is added to your merchant account services.

Payment gateways serve as interfaces between your website and your merchant account provider’s processing network. They send transactions to the processing network so that a purchase can be authorized and transaction processing fees can be assessed. Payment gateways also include a number of very valuable features, from security services that protect your customers’ credit card information to databases that can store your customer’s information (i.e., name, billing address, shipping address, credit card information, etc.) so they don’t have to re-enter it every time they shop on your site.

Support For Multiple Payment Types

Brick and mortar businesses have the luxury of being able to accept cash, eCommerce merchants do not. That means you’re going to have to rely on online-friendly payment methods. The more you can accommodate, the fewer customers you’ll turn away at checkout.

What kinds of payment methods? Credit and debit cards are a given. Some industries will to offer the convenience of taking American Express or Discover if they’re popular among their clientele. Less necessary but worthy of consideration are digital wallets (ApplePay, etc.), which offer more security than the typical online transaction. Businesses that do recurring payments and subscriptions may want to consider eCheck/ACH payments. Finally, if you’re doing business internationally, you should consider a service that allows you to accept payment methods that are popular in those countries.


Chances are you use several different pieces of software to run your business, with each offering a specific advantage. While it’s certainly possible to use all these different systems completely apart from one another, you’ll save a lot of time and repeated effort if they all play nicely together.

Integrations, in other words, are the ability to access one program from within another. Whether it’s through a native integration or an API call, having all your core programs able to talk to one another is a feature you’ll want to consider when looking for an eCommerce-ready processor.

How To Choose The Right eCommerce Merchant Services For You

Of all the services you’ll need to run your online business, merchant accounts are, unfortunately, the most complicated to understand. There’s a lot of terms and jargon that you may not be familiar with, as well as a host of confusing options to choose from when selecting the provider that’s best (and most affordable) for your business. We’re here to help.

Contract Terms

The industry standard for a merchant account a fixed-length contract with an initial term of three years, an automatic renewal clause that extends the contract for one-year periods after that, and an early termination fee (ETF) that the processor will charge you if you break your contract by closing your account early.

However, more and more services are doing away with long-term contracts and allowing customers to go month-to-month. Unless you have a high-risk business, we recommend avoiding merchant services that try to lock you into a contract.

Processing Fees

Figuring out how much you’re going to pay to process a credit card transaction is one of the most complex aspects of understanding any type of eCommerce merchant service.

In all cases, your provider has to deduct interchange fees, which have to be paid to the credit card associations (i.e., Visa, Mastercard, etc.). They’ll also charge their own fees that go to the processor and the merchant account provider, although this is usually only a small portion of your overall processing cost. How they determine your total processing cost will vary from one provider to the next. However, there are four common pricing schemes that are used by almost all providers:

  • Flat-rate pricing: Often marketed to newer businesses, flat-rate pricing is simple and straightforward: you pay the same price for any card-based transaction. This will effectively be a mark-up for some transactions, and a discount for others. Good for starters, but you may outgrow it.
  • Tiered pricing: Different transactions are charged different rates based on tiers. Usually the lowest tier’s price is what’s advertised. We don’t like tiered pricing because there’s no telling what rate an individual transaction will be charged.
  • Interchange-plus pricing: This pricing scheme separates the fees charged by the interchange (the credit card companies) and your processor. We like this model because you’ll know exactly how much your processor is charging you per transaction.
  • Membership pricing: Also known as subscription pricing or wholesale pricing, membership pricing is similar to interchange-pricing except it reduces your per-transaction charge in exchange for a monthly fee. Great for high-volume processing.


Are you already selling offline and want to branch into eCommerce? Or are you starting from scratch and going online-only? That answer may change what you’re looking for from a merchant account provider. If you’re selling offline, you probably already have a merchant account. In that case, you’ll want to look for a compatible gateway and shopping cart support. If you’re starting from scratch, you might prefer an all-in-one service.

Common Questions About eCommerce Merchant Accounts

What is an eCommerce merchant?

An eCommerce merchant is someone who sells products or services online.

What services do eCommerce merchant accounts provide?

eCommerce merchant account providers offer services designed to allow you to sell online. Services include payment processing, a payment gateway, shopping carts, and sometimes webspace.

Do I need both an eCommerce merchant account and a payment gateway?

Small businesses need both a merchant account and a payment gateway if they want to process online transactions.

What is the best payment gateway for eCommerce?

The best payment gateway for eCommerce is the one that plays nicely with your payment processor. Authorize.Net is popular for a reason, though we’d recommend getting them through a merchant services provider rather than signing up directly.

Get Started With eCommerce Merchant Services

Starting an eCommerce business is never easy, but it’s far less challenging today than it was just a few years ago. Whether you opt for a payment service provider or sign up for a full-service merchant account for ecommerce, choosing the right provider is a critically important step in getting your business off the ground.

As we’ve noted above, merchants processing over $5,000 per month in credit/debit transactions will typically save money (and receive better service) with a true, full-service merchant account. Payment service providers such as Square (see our review) are a better choice for those processing less than $5,000 per month. Because PSPs typically don’t charge monthly fees or impose long-term contracts, it’s easy to switch to a genuine eCommerce merchant account once your business reaches this threshold.

For a more in-depth look at specific providers, check out our article, The 6 Best Online Credit Card Processing Companies for Small Businesses, for an overview of our top choices for credit card processors for your online business.

In Summary: The 3 Best eCommerce Merchant Services For Online Businesses

  1. Square: Best for eCommerce businesses that also do face-to-face transactions.
  2. Stripe Payments: Best for tech-savvy eCommerce businesses.
  3. PaymentCloud: Best for high-risk businesses.
Chris Motola

Chris Motola

Expert Analyst & Reviewer at Merchant Maverick
An expert in personal and business loans and financial health, Chris Motola has been writing about small business finance and payments for over 5 years. He has been cited in various industry publications, including Forbes Advisor, GoBankingRates, and Medium. Chris is a graduate of the University of Central Florida.
Chris Motola
View Chris Motola's professional experience on LinkedIn.

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Merchant Maverick’s ratings are editorial in nature, and are not aggregated from user reviews. Each staff reviewer at Merchant Maverick is a subject matter expert with experience researching, testing, and evaluating small business software and services. The rating of this company or service is based on the author’s expert opinion and analysis of the product, and assessed and seconded by another subject matter expert on staff before publication. Merchant Maverick’s ratings are not influenced by affiliate partnerships.

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