Payment Processing for SaaS Companies

Your SaaS business deserves a payment solution as unique as your product offering. Learn which elements are most important in this expert guide.

As a SaaS business owner, you spend your time creating products to make other people’s lives easier. You meet customers where they’re at, providing software so that they don’t need to own or manage complicated technical solutions themselves. 

While most ecommerce companies operate on a one-time sale basis, your business likely uses a more complex pricing model involving subscriptions, as well as per-seat or metered billing. That’s not something all payment processors can support, so you need to be selective when shopping around for the right system. Let’s dig into exactly what to look for to support your SaaS business growth.


What Is SaaS Payment Processing?

Every company needs a payment processor to facilitate the movement of funds from a customer’s account to the business’ bank account. The process is usually fairly simple, with the processor transmitting data about the transaction from bank to bank. 

However, there are more layers of complexity in SaaS payment processing. SaaS companies use sophisticated billing structures to deliver customized solutions to each customer. Your SaaS payment processing may need to support the following features, depending on your business model:

  • Recurring billing
  • Subscription management
  • Multiple pricing tiers
  • Metered pricing
  • Per-seat pricing
  • Prorated billing
  • Rollout of new pricing plans
  • Changes to price due to upgrading or downgrading service
  • Adjustable taxes depending on changing rates

The Benefits of SaaS Payment Processing

Payment service providers create SaaS payment processing specifically to cater to the distinct needs of this type of company. Not only does this individualized form of processing benefit your company, but it also benefits customers. Here’s how.

Easy, Reliable Automated Billing

With SaaS payment processing, you can easily automate recurring billing so that your team isn’t stuck sending out individual bills or chasing down late payments. Plus, SaaS payment processors can expand with you as you add different service tiers or payment plans, unlike a typical ecommerce payment processor.

Integrated Software Environment

You likely already use a variety of technical tools to support your product, business model, and customers. Your payment process has to fit in with those tools for everything to work efficiently. SaaS payment processors allow you to work with the API so that you get flawless integration.

Improved Accounting

Subscription-based companies need to defer revenue until the customer uses or realizes the full service. In other words, a one-year subscription takes 12 months for full use, and your business can’t reconcile that revenue until this is complete. With SaaS payment processing, you can automatically reconcile subscriptions, saving the time and headache of manual accounting.

Boosted Customer Experience

From the customer perspective, SaaS payment processing provides a frictionless billing experience. They get regular withdrawals and consistent service with no effort after setup. They can also easily adjust their plan with a few clicks. Meanwhile, the payment processor protects their stored payment information with advanced security measures, like encryption and tokenization.

The Challenges of SaaS Payment Processing

No solution is perfect, so there are still a couple of key challenges in SaaS payment processing to consider. First, you’ll likely pay a premium for SaaS payment processing. Many SaaS payment processors charge higher-than-average transaction fees that vary depending on different variables, like payment methods. 

If you run a SaaS business with a variety of tiers and offerings, the rate you pay can be very inconsistent and you may even run into hidden fees. All of that considered, it can be hard to estimate what your payment processing will really cost.

Certain payment methods, like ACH transfers, lend themselves to subscription services. As a result, most SaaS payment processors offer a limited selection of payment methods, avoiding options like buy now, pay later (BNPL). Some customers may abandon their purchase with your company if you don’t offer their preferred payment method.

What Should a SaaS Company Look For in a Payment Service Provider?

Flexibility and Scalability

One of the primary elements you need from a payment processor is the ability to bill for multiple pricing plans. Whatever provider you go with, you’ll need to ensure they can provide the flexibility to adapt to your business model.

Likewise, your provider also needs to be adaptable as your business grows and changes. It must be able to support the number of transactions you process now and in the future. You don’t want to potentially experience any service outages later on when business is booming. 


Before choosing a new payment system, it’s important to make sure it can seamlessly integrate with your existing tech suite. Otherwise, you may end up needing to replace other services, which can cost time and money. Make sure the system can integrate with your:

  • CRM
  • Analytics software
  • Accounting or tax management software
  • Payment gateway (if separate from your payment processor)

Payment Methods

As we discussed above, every customer has one or two preferred payment methods. Offering a limited selection of options could mean the difference between winning and losing a sale. Find out whether a payment service provider supports the payment methods your target audience demands before signing up.

Pricing Transparency

You’re in business to earn a profit. Your payment solution shouldn’t eat into your bottom line with expensive fees and hidden costs. Ask your potential payment service provider for a detailed breakdown of the fees. You can also just opt for a provider that uses a flat-rate pricing model to avoid surprise fees. 

Checkout Customization

While your payment processor should allow you to set billing on autopilot, you’ll still want to be in control of your checkout experience to ensure that customers enjoy a seamless process. It’s important to choose a provider with open APIs that your developer team can integrate with. This way, you can add hosted payment fields to your website or app and keep customers within your environment.  

At the same time, your provider should allow you to control your billing and transaction flow so that you can optimize for customer experience. This ultimately helps you avoid friction and convert more customers.

Customer Support

As a SaaS business owner, you know that any tech solution can glitch or experience downtime, no matter how great it is. In the unlikely event that your payment system runs into issues, you need to know that you can easily contact customer service to correct the problem. Consider choosing a provider that offers a dedicated support team to fix issues before they take off.


All businesses need to maintain PCI compliance, which means that you follow the regulations set by the Payment Card Industry Security Standards Council to protect customer information. Rather than managing these complex requirements on your own, your payment service provider can do it for you. This ensures they use industry-standard measures, like tokenization, to protect your customers.

The Benefits of Working with as Your Payment Service Provider 

If you’re ready to switch to a payment solution optimized just for SaaS companies, is a great choice. We combine a powerful payment solution with affordable pricing and robust features, like:

  • Developer-friendly APIs: Integrate with our APIs to add hosted payment fields to your existing business tools for the ultimate custom solution.
  • Frictionless checkout: Keep your customers happy with simple, easy checkouts. The system can remember customer payment information for speedy checkouts and supports recurring billing for subscription services.
  • Inclusive payment methods: offers a wide range of payment methods so that you can give your customers the options they want. Start accepting credit and debit cards, digital wallets, ACH transfers, BNPL schemes, and more.
  • Intuitive dashboard: The Pay Dashboard provides you with the in-depth customer insights you need to turbocharge your business. Get information about your revenue, cash flow, KPIs, customer preferences, and more - all in one easy-to-use tool.
  • Advanced security: maintains Level 1 PCI DSS compliance. We use top-tier security measures, like tokenization, encryption, and multifactor authentication to protect your business from fraud.

Click here to sign up for now!

The Bottom Line

Your SaaS business provides advanced solutions to your customers. Make sure you have a cutting-edge payment solution that can keep up with your complex offering. With SaaS payment processing, you can get the flexibility, scalability, security, and integrations necessary to provide the best customer experience.

Get the robust payment solution your business model demands by switching to With our solution, you get progressive fraud protection, customizable systems, and advanced customer insights. Plus, it won’t cut into your profits. provides affordable, flat-rate pricing, so there’s no limit to your business growth. 

Click here to get started with now!


What's the best way for an SaaS company to accept online payments? provides a powerful payment solution perfect for the distinctive needs of SaaS companies. You get access to our open APIs, keeping you in control of the customer’s billing experience. Plus, your customers get a frictionless checkout experience, recurring billing, and secure transactions. Click here to find out how you can get started.

What's an example of an SaaS pricing model?

Per active user pricing is an SaaS pricing model in which customers only pay for the service they use. For example, they can sign up for 100 employees to start without an upfront bill. They pay only for the number of employees they actually had using the service at the end of the year, even if it was less than the initial agreement.

What are the steps in payment processing?

Payment processing includes the following steps:

  1. Customer enters payment details.
  2. The payment gateway encrypts the payment details, then transmits them to the customer’s bank or card issuer for authorization.
  3. The bank or issuer approves or declines the sale via the payment processor. 
  4. If approved, the bank or issue releases funds to the merchant’s bank account via the payment gateway.

What payment methods are common for SaaS?

Credit cards, direct debit, and ACH transfers are the most common payment methods for SaaS, since they easily support recurring payments.

Meet the author
Ginny Dorn
Ginny Dorn is a finance and business copywriter specializing in credit card processing and fintech. She graduated from Western Illinois University with a bachelor's degree in family and consumer sciences.
A Robust SaaS Payment Solution is a powerful, full-service payment solution. It provides critical tools for SaaS business growth, like industry-standard security features, developer-friendly APIs, frictionless checkout, and advanced analytics.

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