Best E-Commerce Business Bank Accounts

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The global COVID-19 pandemic set the stage for the e-commerce business boom. Coupled with advanced features in the industry that make online shopping more accessible and safer, e-commerce sites have been raking in massive profits. But like every other business, they have had their fair share of challenges, and for the e-commerce sector, most of these challenges are about receiving payments and accessing proceeds from their business.

Unlike brick-and-mortar businesses, the financial needs of e-commerce businesses are rather unique. This means most traditional banks won’t touch them, particularly those that deal in uncommon items and services. Lucky for them, the technology boom hasn’t been on e-commerce sites only. Fintechs or challenger banks have also come up over the last couple of years, and they offer quite an impressive service range, most of which covers the needs of e-commerce businesses. All that is left is for the businesses to choose the best business accounts for e-commerce businesses.

If you’re still trying to sort through the different options, here’s a look at some of the best business accounts for e-commerce that you should consider.

Does Your E-Commerce Business Need a Bank?

Yes! Your eCommerce business needs a bank. And not just any bank, the best one. It will help you manage finances effectively and provide a secure payment gateway for your business and customers.

A good e-commerce business account is a secure way to manage your business’s financial activities, including tracking cash flow, paying suppliers and even managing payroll. With a business account, you also enjoy separating your personal and business finances, which is crucial for accounting and tax purposes.

Best E-Commerce Business Accounts

Pay iO

It’s almost impossible to discuss online business banking without mentioning Pay iO. Unlike most of the other options we will discuss, which offer amazing banking services, you will notice that most don’t offer business banking as a primary service. It’s just a market gap they want to take advantage of.

Pay iO, on the other hand, is designed for small and large businesses and has just the right features for e-commerce businesses.

Being a fully-fledged online bank, Pay iO offers an extensive range of features that benefit e-commerce businesses of all sizes.


Business owners can access their accounts via mobile apps or the web, giving them unrivalled access to their funds wherever and whenever. The account has great features for startups and established startup e-commerce businesses, such as getting bank payments directly from your customers and the ability to manage your expenses and transactions from one convenient place.

Another feature that sets Pay iO above its competition is the ability to receive global payments. This is vital for e-commerce businesses because they market globally and have customers purchasing their products worldwide. The ability to process payments in different currencies is a huge advantage.

Also, you can hold a multi-currency account for most major currencies, saving you the trouble and cost of changing currencies back and forth. Additionally, Pay iO allows you to manage your account conveniently, reducing administrative time and effort.

Besides using your Pay iO account to receive payments from your customers, you can also use it to run the expenses of your business. The account provides a digital wallet, dedicated bank details and a business card. All are free, fully online and hassle-free.

If you need to exchange currency to pay suppliers, Pay iO offers you the real mid-market rate with just one low fee to exchange currencies, saving you from exorbitant fees. The challenger banks also offer fast and simple multi-currency bank transfers. With a vast global network, you have an account everywhere, making payment processing easier and faster.


Novo is another great option built mainly for business owners, entrepreneurs and freelancers. Novo’s wide array of integrations with some of the market-leading software services is a dead giveaway to the account’s dedication to businesses.

Some of the current integrations with Novo include;

  • Stripe
  • Shopify
  • Xero
  • Quickbooks
  • Amazon
  • eBay

Like many challenger banks on this list, Novo has no physical location. However, they do have a responsive customer support staff that can help you work through any challenge you might be having on their platform.

One of the benefits of using Novo is its free business checking account, which is perfect for budding e-commerce businesses. With no monthly fees and minimum opening deposit requirements, it’s one of the best banks for eCommerce businesses.

Other perks you will enjoy by opening a Novo business account include;

  • Free ACHs, mailed checks and incoming wires
  • No hidden fees
  • A mobile app to handle transactions on the go
  • Unlimited ATM fee refunds
  • A virtual card
  • Insured deposits

The only downside to having a Novo business account is that it doesn’t accept cash deposits. But for e-commerce businesses where most of the transactions are online, this shouldn’t be much of a problem. If you have to deposit money, it’s possible through Novo’s mobile check deposit feature or by purchasing a money order through an approved vendor.


Sometimes, the best banking solutions are not the most popular, and Mercury is living proof that with the right banking partner, a business can thrive, even when that banking partner is not popular but offers the right features.

Mercury is explicitly designed for startups and offers various features, including integrations with Shopify, Amazon, QuickBooks, Xero, PayPal, Stripe and others, taking care of most administrative and payment processing tasks.

It provides an open API access, allowing the business to customise and automate the account by creating various transfer rules, making bulk payments and reconciling transactions.

With Mercury, businesses can access in-built digital tools that let you send and receive payments. Additionally, you can monitor spending and also track transactions. The account also allows you to create virtual debit cards for temporary usage, add them to your mobile wallet, edit spending limits and freeze your card through the app. It has all the safety and business features you want in one convenient location.

Mercury offers business checking and savings accounts. There are no minimum opening balance requirements, which is a huge benefit for small businesses that might land in a cash crunch frequently, and there are no monthly fees as well. Like Novo, Mercury doesn’t accept cash deposits. Other reasons you should consider opening a Mercury eCommerce business account include;

  • No monthly fees or minimum opening deposit
  • Unlimited fee-free transactions
  • Free domestic and international wire transfers
  • Open API access to customise your banking
  • 100% online banking

You can also use Mercury Treasury instead of a traditional savings account to earn up to 4.65% annual percentage yield on your idle cash.


PayPal is a long-standing, popular and trusted choice among digital banks. Its main benefits include a robust, user-friendly platform that simplifies sending and receiving money globally. The platform established its reputation as a versatile and comprehensive solution for managing your eCommerce finances by offering features such as convenient invoicing, easy checkout solutions for your online store, and you also get a business debit card.

PayPal has plans for small-to-medium businesses that offer varying features depending on your chosen plan. Some of the features offered include invoicing and customer support.

The enterprise plan caters to larger organisations with a high transaction volume. It provides them access to custom solutions, advanced reporting and dedicated support to manage their extensive e-commerce needs.

One of the biggest benefits of working with PayPal is no monthly fee. Instead, it operates on a pay-as-you-go system, which is hugely advantageous to small businesses without many transactions. The fees for the services depend on the transaction type and location, and there is an international sales fee that applies besides the domestic fees. There are also separate fees for additional services like chargebacks and recurring billing.

While many people are content with its range of services, there have been numerous complaints about PayPal suddenly withholding funds and closing accounts without proper explanation. Because of this, PayPal has received low ratings on several third-party review platforms.

Wise Business

This is a unique account that eCommerce businesses can use to receive funds in up to nine different currencies without any additional costs. It’s an excellent account for businesses on a cost-cutting mission that don’t want to sacrifice convenience in the process.

For a one-time fee, a Wise Business Account allows you to access major currencies such as USD, GBP, AUD, CAD, and EUR, among others. Once you receive the funds, you can conveniently spend or send them in the original currency or convert them to numerous other currencies as needed.

Wise Business is known for its competitive market rates compared to other services. However, it’s not just about the fees but also the many handy features that businesses also access, like the accounting software integration and a business debit card. Should you need foreign currency, Wise will offer you the mid-market rate.

Wise Business doesn’t offer different price plans. Instead, it has various features and services with individual fees and charges, ensuring businesses only pay for what they use, making this an affordable and flexible option.

Fees on Wise are transparent and competitive. However, opening a business account on Wise is not free, but the cost is not extremely high either. 

When working with Wise, you should know that their card is unavailable for all countries, and not all currencies are supported. Also, you can fund transfers using cash or cheques. But these are quite common drawbacks among many challenger banks.

What to Consider Before Opening an E-Commerce Business Account

From this short list of the best digital banks for eCommerce business accounts, you can see plenty of options available. Each option appeals to different businesses and has different features.

Choosing the right one might be challenging with so many features to consider. But there are some important factors that you should overlook when shopping for the best eCommerce business bank account. 

Your business needs

You must first remember your business needs when shopping for a bank. Understanding your needs makes it easier to find the right account.

If you’re a startup looking to keep overheads low, a free business checking account can be helpful. Most established businesses may go for major banks because of their reputation, not to mention the banking fees, which are not a major concern for them.

Because not all banks are the same, you should keep your needs at the forefront and go with a bank that best matches and meets them.

Fees and pricing

Every business account charges a fee at some point. These can be monthly maintenance fees, ATM fees, currency exchange fees, and some will even charge non-sufficient funds.

Some banks often waive these fees when you meet certain requirements, such as maintaining a minimum daily or monthly balance or setting a specific number of monthly deposits.

If saving is at the top of your list, go for banks with the lowest fees. Some don’t even have monthly fees and only charge you for the transactions you make.

Convenience and ease-of-use

Digital banks are notorious for convenience. But not all of them are easy to use. When choosing an eCommerce business banking solution, go for one with a mobile app or offers online banking. Make sure you read what other users are saying about the bank by reading reviews from previous customers. This should give you insight into the bank’s user experience.

Transaction speeds and limits

Many banks impose transaction limits on business and checking accounts. You may have to pay a small fee if you exceed that limit. This is a crucial factor to consider depending on how fast your business grows and how fast you can transfer funds to your main account.

You don’t want to work with a bank that will bring your operations to a halt once you hit your daily transaction limit. If you know you conduct high volumes of transactions, you should look for a bank that allows unlimited transactions to avoid fees.

Global accessibility

The main idea behind eCommerce was to break through boundaries and make the world a single shopping mall. This benefit is not achieved if your customers can’t make payments from wherever they are and you can’t access your business account anywhere.

Managing your finances on the go is a crucial aspect of eCommerce businesses. Ensure you can access online and mobile banking and have 24/7 access to your bank account.

Payment integrations

You need more than just a standard business account with an eCommerce business. You need an account that integrates with other business software systems such as Wave, QuickBooks, Shopify, and Amazon. Before settling on the account, find out if you can sync your existing business software. The more software and tools you can sync, the easier it is to streamline your business finances.

Access to business and reporting tools

A good e-commerce business bank account should offer access to various business and reporting tools that make running a business easier. For instance, a business checking account may have bookkeeping features that automate profit and loss statements and income and expense reports. These tools can lessen administrative work and make business operations more efficient.

Think beyond your current needs

When opening a business account, it’s easy to get caught up on what you need now because it is what matters at the moment. But don’t forget to consider whether the account or bank you choose can grow and keep up with your business.

Select an option with many features that you can use in the future to help your business grow. Most digital banks with tiered services like Pay iO often have these features and set up their service to allow the business to keep scaling their service as they grow.

Consider the basic services you’re getting.

Before opening an e-commerce business account, consider the basic services you are getting. At a minimum, the account should offer the following basic services;

  • Checking account – To deposit and withdraw funds for daily transactions
  • Savings account – For storing excess funding not currently in use
  • Credit card and debit card – To manage the daily spending of your business
  • Online business banking – To give the cardholder access to electronic banking services

Some banks will also throw in a payroll account for larger businesses to make it easier for them to meet payroll without any challenges.

Final Thoughts

Choosing an e-commerce business account isn’t something you should take lightly. The decisions you make now will likely determine the growth of your business for the next couple of years and could either fuel growth or stunt the business. Also, moving banks isn’t the easiest process and might create confusion, especially when working with digital banks, and could even result in some downtime for your online business.

You need to proceed cautiously and consider all your needs and wants. Only work with banks that meet your requirements and have your business’s best interests at heart. Of course, this might take some time, but the five options highlighted above are a great starting point.

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