Ecommerce Merchant Accounts: What to Look for in Your Payment Partners

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Online success depends on conversion — and what’s one key element to converting customers? Having the right ecommerce merchant account.

For many, when we think about ecommerce payments, we think of traditional payment processors and payment gateways. However, this is a trend that is quickly shifting.

With 74% of B2B customers saying that they would switch to a new B2B ecommerce site entirely for better purchasing options, ecommerce merchant accounts are quickly taking advantage by offering a multitude of payment options and streamlining the entire purchasing process.

Ecommerce merchant accounts — referring to accounts where ecommerce businesses can accept online payments — are built to help you tailor your business to consumers’ expectations.

Why Modern Business Needs Ecommerce Merchant Accounts

The ecommerce industry has surpassed the single offering of credit and debit card transactions.

Between businesses' heightened complexity and modernization — especially in B2B — enterprises are increasingly recognizing the need for ecommerce merchant accounts.

Online business presence.

Since the early 1990s, online businesses have grown exponentially — to the point where nearly every business you interact with today has an online presence.

While the Internet has given massive growth opportunities to businesses worldwide, it has also presented new challenges — for instance, managing payments digitally.

Getting your customers to the shopping cart is one goal, but getting them to convert requires the right digital payment options.

Multiple options for payment.

In a world of increasing convenience, options are everything.

With the rise of online purchases, digital payment companies have begun to sprout up, offering their services for credit card payment processing for a small fee.

However, those small fees can add up quickly when you want to offer your customers various options. Utilizing a merchant account provider can help manage and reduce those costs versus working with different gateways that each charge separate fees.

Increased need for security and accuracy.

While convenience and options are essential to consumers, security takes the cake.

It’s crucial that your customers feel confident in processing payments on your website. Without trust, you won’t see many sales.

As security becomes an increasingly important factor to consumers, ecommerce merchant accounts have focused on making their services secure and typically use the highest grade encryption to maintain PCI compliance.

What Services do Ecommerce Merchant Accounts Provide?

Digital payments are vital to the success of your business.

Business owners will need to offer a variety of payment options and a high level of security for digital transactions to fuel online success.

Before accomplishing that, you should understand what to expect from partnering with an ecommerce merchant account?

Payment processing.

This is arguably the most important benefit.

By working with an ecommerce merchant account, you’ll have a way to process the payments your customers submit on your website — confidently and securely.

Encrypted payments.

The importance of security cannot be stressed enough. The good news is that the majority of ecommerce merchant accounts now come with encrypted processing, meaning that you and your customers are safe when making a transaction.

When researching what ecommerce merchant account may be suitable for your business, make sure they handle encrypted payments.

POS systems.

Are you a retailer with both an online and offline presence? You’re probably wondering what an ecommerce merchant account means for your point-of-sale (POS) system.

Luckily, some ecommerce merchants like Stripe or Square have POS systems available, bringing in an added benefit of streamlined inventory management.

Easy-to-use software.

Just like the experience you give your customers, your experience with ecommerce merchant accounts should come with easy-to-use software.

The software should include tracking payments, issuing refunds and seeing reports from one easy-to-view dashboard.

A streamlined payment experience.

The key to online success is making processes and experiences as simple as possible — for you and your customers.

A streamlined payment experience will not only help you become more efficient, but it will leave your customers with a positive brand affinity.

What Types of Fees are Associated with Merchant Accounts?

When selecting an ecommerce merchant, know that there will be fees associated with them, including:

Setup Fees.

Ecommerce merchants will often charge a one-time fee upfront for the initial setup.

The setup fee often depends on several factors, like what bank account your business is using, your sales volume or what type of checkout software or hardware you have.

Maintenance Fees.

Some merchants will charge you an ongoing fee for maintenance services, especially if you're using any software tools.

Maintenance fees are likely to come at a flat, consistent monthly cost and are separate from transaction fees.

Transaction Fees.

When completing a payment, it’s easy to forget how many people along the process want a cut, from ecommerce credit card processing companies to payment processors. Because of this, transaction fees are likely to be the most costly when setting up your ecommerce merchant account.

There are several ways ecommerce merchants handle transaction fees, including:

  • Flat rate fees: Flat rate fees are straightforward — no matter what you pay for, you will receive the same rate for any transaction that occurs.

  • Tiered fees: With tiered fees, you’ll pay different fees depending on the tier a purchase falls into and its risk. These tiers are broken down into three categories: qualified, non-qualified and mid-qualified transactions.

  • Interchange plus fees: The most transparent transaction fee, they typically include the exact costs to process a payment and any associated fees

What to Look For When Choosing a Merchant Service

Finding a merchant service to choose from is not always a simple nor an easy process. When selecting one, make sure to look for:

Simple integrations.

You’ll need an ecommerce merchant account with a payment processor that syncs up to your site quickly.

If you have BigCommerce, you instantly have access to ecommerce merchants such as Paypal, Square, Amazon Pay, Apple Pay, Chase Pay, Adyen, Authorize, Stripe or Cybersource.

With all of these options available, your ecommerce website will be natively equipped to handle optimal digital transactions.

Multiple card and international processing.

Despite the growing prevalence of digital payment systems, traditional payment methods are still crucial to your payment offering.

You’ll need an account that takes many cards — such as Visa, Mastercard, Discover, American Express, etc. — and handles other payment services like PayPal or Apple Pay.

Even if you don’t currently sell internationally, choosing an ecommerce merchant that can handle international card payments, such as Mastercard’s Maestro, is still essential.

State-of-the-art encryption and security.

Security is one area that you cannot scrimp on when selecting an ecommerce merchant. The difference between a secure and unsecure network can make a world of difference for both your company and customers.

When researching what ecommerce merchant account may be right for your business, make sure they handle encrypted, secure payments. The good news is that the majority of ecommerce merchant accounts come with encrypted processing.

Low fees.

While you may prioritize handling your customers’ cash, you must look out for yours, too.

Your payment processor will most likely charge you each time you make a sale, so ensure you’re setting up a merchant account with low fees. When selecting a merchant, consider how many sales you're likely to make and calculate the estimated cost to give you a more realistic outlook.

Customer support.

When something goes wrong, you need support — and you need it fast.

With many merchants out there providing 24/7 support staff or AI-driven chat options, plenty of options are available. Understanding those support options with each merchant is vital to your business.

Top Trustworthy Ecommerce Merchant Accounts

There are many ecommerce merchant accounts available to choose from. The following are a few of our favorite ecommerce merchant accounts:


Square is a commonly recognized merchant, seen by consumers at many offline retailers. The beauty of this merchant is that you can benefit from a connected POS system without any monthly fees.

The payment solution accepts all major credit cards, Apple Pay, Android Pay, debit cards, gift cards and prepaid cards. They deposit funds from your sales as soon as the next business day, versus waiting 2–6 business days like many other POS solutions.

Additionally, Square complies with PCI DSS to ensure your business stays secure.


In addition to traditional credit and debit cards, Stripe works with Google Pay, Apple Pay, and Masterpass, and handles international payments with ease.

When it comes to security, Stripe is PCI compliant — meaning it has achieved best-in-class security certification across the payments industry.


If you’re looking for more straightforward pricing, Adyen may be the best option. The merchant primarily offers credit and debit card payments, though it has recently expanded into digital payment options like Apple Pay and PayPal.

The online payment gateway can process payments on online stores, mobile and in-store, in addition to processing transactions across 200+ countries and territories.

Adyen currently supports over 250 local payment methods — including ACH — and 37 currencies, including ACH. provides direct connections to card brand networks, which optimizes response times and minimizes your data security risks.

In addition, you will be able to accept international transactions from customers worldwide. The only catch? Your business must be based in the United States, Canada, United Kingdom, Europe, or Australia. makes it easy for customers to pay with their preferred payment option, including all major credit cards, signature debit cards, e-checks and digital payment solutions.

Regarding security, provides advanced fraud detection and secure customer data storage with every plan.


With Cybersource, you’ll be able to improve your business agility, control risks and take advantage of all the capabilities that can help you increase sales on your ecommerce website.

Cybersource has a worldwide processing network of more than $500 billion — reaching regional and international markets has never been easier. 

Plus, the platform’s flexibility allows you to respond quickly to changing market conditions. You can easily add or switch devices and terminal systems, payment types through a single API and payment processors.

The Final Word

Whether you are a small business or a larger retailer, payments are a core component of your success. Make sure to avoid poorly implemented payment processing solutions and focus on finding an ecommerce merchant service provider that can support your current and future business plans.

With BigCommerce, you gain instant access to ecommerce merchants worldwide, along with more than 65 pre-integrated online payment solutions, serving 230 countries and over 140 currencies.

No matter which ecommerce merchant account you want to use, BigCommerce will be there at the click of a button.

FAQs for Ecommerce Merchant Accounts.

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