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How to Select the Best Online Payment System for Your B2B Business?

B2B paymentsSaaS FinanceAccounting and Software

Côme Chevallier

Apr 26, 2024


What you should consider when selecting the right online payment systemThe best online payment gateways on the market Key takeaways 

An online payment processor is a gateway that processes your business's payments. You can think of it as a middleman between your business and your customers. 

Fueled by the digitalization of payment methods, online payment systems have become a staple in B2B payment strategies. Offered by fintech companies, these online payment platforms have disrupted the payment market, making online payments a walk in the park. 

With these platforms, online payments are completed in just a few clicks. Online payment gateways not only make for a better customer experience but also help get your business paid faster. 

With consumers growing accustomed to this technology, It’s important that B2B businesses keep up.

But where do you start? There are many solutions on the market and it’s not easy to know how to choose the right one that fits your business needs. 

With that in mind, read on to find out the answers to the following questions:

  • What criteria should you look for when selecting your payment system?

  • What are the best online payment gateways?

  • Which one should you choose for your business?

Let’s dive in! 

Upflow is an accounts receivables software that helps B2B businesses with their cash collection. Our solution supports a range of online payment gateways and, in March 2024, we launched our own next gen payment processing platform integrated within our solution.

We call it Payments by Upflow.

Payments by Upflow brings a powerful yet simple and frictionless experience to B2B payments. By seamlessly integrating within the Upflow platform, our merchants can offer online payment options instantly to all their customers.

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What you should consider when selecting the right online payment system

Start by identifying the criteria your business will need to consider for its payment gateway. Some points include: 

  • Security: Payment security should be a top priority for any business. You’ll have to make sure that your customer's credit card or payment information stays secure. Depending on the online payment solution you choose this might fall in the hands of your payment gateway's responsibility or yours. 

  • User experience: The key to your business getting paid is making the payment process as easy as possible. You’ll need to consider what online payment methods your customers might be used to using or already have an account with. Remember, the chosen software should be intuitive to offer a user-friendly experience.

  • Pricing: Depending on your business model and if you are an SME or large enterprise different payment systems will be better suited for you. Some payment solutions will be best suited for businesses dealing with small transactions. The opposite can also be said for larger businesses. 

  • Currencies: Not all online payment systems are created equal when it comes to the currencies they support. On top of that, some processors might add additional fees to support different currencies. 

When selecting your payment processor, remember that it’s not just about providing a way for your customers to pay you. It is also about how the payment system will have an impact on your electronic invoicing, tracking, accounting, and more

Your selected online payment system will have an impact on your business’s long-term growth and scalability. The key is to identify your current needs but also forecast what your future business needs may be.

The best online payment gateways on the market 


You’ve probably heard of Paypal before. This payment provider is one of the leading players in the market with over 305 million global users. Paypal is an eCommerce company that facilitates payments between its user's in exchange for a small transaction fee. 

After setting up a PayPal account, users can start making payments via their credit or debit card. Paypal is simple and easy to use making it a positive checkout experience. It’s a top choice for both businesses and customers.

Why use it?

Many of your existing customers probably already have a PayPal account making it a good choice for your business. This definitely gives this payment processor a competitive edge over other options. It is already used by more than 17 million businesses worldwide. 

With PayPal, you know your payments will be in good hands. The company takes care of payment security, giving you peace of mind when it comes to keeping your customer's payment information secure. Instead of storing your customers' credit card information yourself, they do it for you. This is a huge advantage compared to other processors

On top of that Paypal allows your customers to connect multiple payment methods making payment a whole lot easier for them. On top of that, this gateway offers many API integrations that easily connect to your business’s invoicing platform.

Who do we recommend it for? 

With PayPal being available in 202 countries, we recommend this platform to businesses with a large international customer base. The platform probably also offers the largest options of currencies. A total of 56! 

What are the downsides? 

The downside of this online payment solution is that its processing fees are about 2.9% per transaction.

Cash Collection on Runway


Stripe is probably the most flexible and comprehensive online payment system on the market. It offers online businesses an easy and efficient way to accept online credit or debit card payments like visas and MasterCard. 

Why use it?

Similar to PayPal, Stripe acts as a processor and makes sure your customers' payments are processed safely and securely.

This payment platform operates on a global scale and can support over 135 currencies with multiple payment methods. 

Setting it apart from other online payment systems is its customizability. Stripe gives its customers developers the tools to create and deploy a personalized payment platform. This means you can create a gateway that matches your business needs. Some of these features include: 

  • Fraud detection and dispute options

  • Reconciliation

  • Reports and insights

  • Third-party integrations

On top of that, it is reputable for its easily accessible customer support team. 

Who do we recommend it for?

Our take on this gateway is that it’s great forth both small and large businesses alike. Thanks to its flexible pricing and customizability this option can be budget friendly to different-sized businesses and their needs. On top of that, it offers many seamless integrations with your finance stack. 

Upflow offers native integration with Stripe allowing your finance team to reconcile invoices with payments in almost real-time automatically. Curious to know more? Take a look at our integration page. 

What are the downsides?

Customization is great but it can be tricky when you don’t have a developer at your disposal. Stripe’s features can be a powerful advantage but can also be considered a disadvantage if you don’t have the bandwidth. Take this into account when choosing your online payment system

How much does it cost?

Stripe has two payment models: 

  • Integrated: This model charges you a 2.9% fee per transaction plus 30 cents for every successful charge. 

  • Customized: This model allows you to create a subscription that best fits your business payment requirements. Pricing is determined by your plans set up. 

Amazon Pay 

It’s no surprise that Amazon pay is another leader in online payment systems. 

Similar to PayPal and Stripe, Amazon Pay directly processes customers' online transactions via their payment method gateway on third-party websites.

Why use it?

Payments are facilitated thanks to using customers' pre-stored payment information via their amazon accounts. This means your customers can easily pay you in just a few clicks by simply logging into their accounts.

Here are some features that Amazon Pay offers merchant accounts:

  • It can easily be set up on your website. 

  • This payment system is optimized for both mobile and voice search (Hello Alexa)

  • It supports recurring payment options. 

Who do we recommend it for? 

Amazon pay is an excellent online payment system option for businesses that often use Amazon. Even better if you know that your customer base regularly uses amazon or has an Amazon business account.

What are the downsides?

Due to its high costs, especially if you are an international business residing outside of the US, we recommend this payment system for larger companies. If your business follows a subscription-based payment model, this gateway could also be a good match for you.

How much does it cost?

Amazon Pay fees are transaction-based with a 30-cent authorization fee: 

  • Domestic fees within the US are 2.9% for web and mobile payments and 4% for Alexa.

  • International fees are 3.9% for web and mobile payments and 5% for Alexa.

Payment Reminder Templates


Square was a trailblazer. They were the first to introduce point-of-sale (POS) credit card payment swipers (paired with an app). This device attached to a cell phone can process payments. 

Since then, their technology has expanded from contactless payments to offering businesses online payment services. Their technology works similarly to the payment options we’ve already talked about.

Why use it?

Here are some features that Square offers: 

  • Fully customizable to your business needs. 

  • Safe and secure payment processing. 

  • It’s simple to use and user-friendly.

  • Helps you set up an online store or online business. 

Who do we recommend it for?

We recommend using Square as your online payment system if you are a small business owner. They are one of the best alternatives to PayPal. On top of that, they offer a free chequing bank account, an online app that provides great analytics, to gift cards. Not to mention they are the only payment solution that also offers in-person payment solutions.

What are the downsides? 

We don’t recommend this option for big companies handling large transactions. Their business model heavily caters to small businesses and is not set up to deal with large accounts. On top of that their pricing model can be expensive for larger businesses.

How much does it cost?

Squares online payment processing service fees are 2.9% plus 30 cents per transaction.

Apple Pay 

Apple Pay has grown in popularity and with about 16.2% of US residents using this method it is definitely an online payment method worth exploring. 

Their unique payment authentication feature gives them a competitive edge over other payment gateways. 

Why use it?

Thanks to Apple’s smartphones Touch ID and facial recognition features, customers can make payments faster and securely. The one-click checkout process skips the need to enter time-consuming cardholder details compared to traditional methods. Instead, the information is directly stored in the users' digital wallets.       

This option has 0 fees for businesses that use it as their online payment processor.

Who do we recommend it for?

Thanks to its no fees policy, we recommend this option to small businesses just starting out. It’s a good and reliable option to quickly get paid by your customers online.

Once you are more established, we suggest you switch to a processor that offers more features. These could include analytics and integrations into your finance stacks such as QuickBooks or NetSuite.

How much does it cost?

This option has 0 fees for businesses that use it as their online payment processor.

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Key takeaways 

  • You’ll have to keep in mind several criteria when selecting your processor: security, user experience, compliance, pricing, currencies, etc.

  • Keep in mind that you must fulfill your current payment system needs but also think about your future ones. Make sure your payment stack can scale as your B2B business grows. 

  • Many payment processors are available to you. It is your choice to select the solution that is right for your business model. Each option comes with its own advantages and disadvantages. 

  • Make sure you select a payment system that will integrate well with your finance stack so you don’t create additional work for your finance team. For instance, Upflow has native integration with Stripe.

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