Payment solutions for SaaS: How to choose the best one for your business

November 19, 2025

Patrick Huynh

CEO

If you’re a software-as-a-service platform (SaaS) researching payment solutions, you’re likely trying to find a better payment solution.

Maybe you started offering payments without a clear payment strategy, and now you’re interested in turning payments from a burden to a growth-engine. But you’re struggling to identifying the right SaaS payment solution for you.

To give you clarity on the best solution for your business, this guide will cover:

What are your payment solution options as a SaaS?
Why embedded payments are the best choice for most SaaS platforms
What are the best embedded payment providers for SaaS?
How Fiska helps you set up and earn income from payments

Fiska is an embedded payments provider that can help you set up payments for the first time. We only work with SaaS companies, and we’ve helped dozens of platforms earn an income from payment processing. Interested in working with Fiska? Book a no-obligation call with a member of our team.

What are your payment solution options as a SaaS?

Using a payment platform

There are many payment platforms that let you accept card payments quickly with minimal setup. After a single integration, transactions are typically routed through the provider’s hosted checkout or API, which means customers complete their purchase in a third-party experience rather than one you control.

This model is popular because it’s fast to adopt, requires little technical effort, and supports a broad range of payment methods, including cards and digital wallets. Stripe’s out-of-the-box setup is a well-known example of this kind of simplicity.

The tradeoff is that you don’t control pricing, you can’t automate how different payment flows behave behind the scenes, and any processing revenue sits with the platform. Because it’s a third-party experience, you also give up control over branding and support.

For early-stage companies and SaaS start ups that just need to accept payments quickly, this approach works well. But as you scale—and want more flexibility, monetization options, and control over your user experience—it becomes limiting compared to more customizable embedded payment solutions.

Becoming a PayFac

A Payment Facilitator (PayFac) is a business that operates as its own master merchant account, allowing it to underwrite, onboard, and manage sub-merchants directly. Each new merchant receives a sub-account under your umbrella, giving you full control over pricing, settlement, and risk management.

However, becoming a PayFac is costly and complex. Registration with Visa and Mastercard alone can exceed $150,000, with 6–12 months of setup and multiple full-time compliance staff required. You’ll be responsible for KYC/KYB, chargebacks, fraud, and ongoing regulatory audits, all while maintaining PCI-DSS and AML compliance.

For most SaaS companies, the risk and setup are just not worth the benefits (especially when you can achieve the same results with simpler payment solutions).

PayFac-as-a-Service

The PayFac-as-a-Service model lets you “rent” PayFac capabilities instead of becoming one yourself. You onboard merchants under your provider’s master account while they manage underwriting, compliance, settlement, and risk. This removes much of the regulatory and financial burden associated with full PayFac status.

You can launch within weeks (rather than waiting months), and you don’t have to pay for full PayFac registration. However, you do get reduced control over branding, limited pricing flexibility, and higher per-transaction fees compared to owning your own PayFac infrastructure.

This model is ideal for mid-stage SaaS platforms or marketplaces that want to embed payments quickly without taking on regulatory risk or heavy compliance responsibilities.

Embedded payments

When you embed payments, you’re building payment processing directly into your SaaS platform. Users are never redirected to a third-party website, which means you control their entire checkout experience.

This model turns payments into a built-in revenue stream. You can generate recurring income through markups or revenue-share agreements (depending on your provider), and offer fully white-label payments so they appear to be an extension of your product.

Integration typically uses a provider’s APIs to connect your platform to the payment network. Once integrated, your provider handles compliance, settlement, and reporting in the background. The setup requires some technical integration effort, but with the right partner, you can launch payments within weeks.

Embedded payments are best for scaling SaaS companies looking to create meaningful, long-term revenue streams.

Why embedded payments could be the best choice for SaaS platforms

You can turn payments into a new revenue stream

Embedded payments enables you to start earning revenue from every transaction that passes through your platform. For instance, if your platform supports a revenue share, you split the profit from the margin above interchange.

This allows you to monetize payments without having to raise your prices to uncompetitive levels.

For instance, when you use a platform like Stripe, you will have to set pricing at 2.9% + $0.30. If you want to take home any revenue for yourself, you’ll have to price over that. However, that is too expensive for most merchants.

But if you use a platform like Fiska, that offers a true revenue share, you can still price at 2.9% + $0.30, but you take home part of the revenue above interchange. This transforms payments from a black box into a brand new source of scalable revenue.

Increase your platform’s stickiness

When payments are embedded, your platform becomes the financial backbone of your merchants’ business. Every sale, refund, payout, and report happens within your platform, making it more inconvenient for users to leave since switching would disrupt their cash flow and daily operations.

Being an all-in-one operating system improves your merchants’ efficiency, reduces friction, and deepens their reliance on your software. By removing the need for outside payment tools, you make your platform more convenient (and therefore more valuable) to every business that runs on it.

Additionally, a white-label payment infrastructure reinforces your brand at every customer touchpoint, meaning merchants will associate payments with your SaaS, not a third-party processor. This helps create a consistent customer experience throughout your entire platform.

What are the best embedded payment providers for SaaS?

You might feel overwhelmed when deciding which provider is right for you. Of all the options out there, how do you know which is best?

To help, we’ve listed three embedded payment providers for SaaS:

1. Fiska

Fiska is an embedded payments partner built exclusively for SaaS platforms. We launched in 2019 after realizing most payment providers were built for retailers first, then retrofitted for software. That left SaaS founders with rigid systems, limited customization, and poor support.

We started Fiska to fix that, and our goal is to make embedding payments both profitable and simple.

We do this by entering into a true revenue share partnership with our partners:

We add a small percentage markup to our payment processing costs
When your merchants process sales through your platform, they get charged the marked-up rate
We pay the card networks the true cost of each transaction and keep the markup as gross profit
We share a percentage of the gross profit with you

We don’t charge platform fees, so once you integrate with our API, you create a recurring revenue stream. This creates a great foundation for partnership, since we all benefit from mutual success.

When you choose Fiska, you also get:

Full support from a dedicated team of payments experts

At Fiska, we understand how complex payments can be, which is why we provide every partner with access to a dedicated, ongoing support team comprised of experienced payments professionals.

We’ll schedule regular check-ins with you to ensure we stay up to date with your plans and have plenty of opportunity to share our expertise. Think of us as your fractional Head of Payments: we’ll take the time to show you how payments work, recommend a pricing model, and help you put together a payments strategy.

You can reach us via Slack or email, and we also offer level 2 merchant support. If your merchants encounter an urgent payment issue you can’t fix, we can step in and resolve it.

Fast launch within weeks with our single, omnichannel API

Fiska uses a single omnichannel API that unifies online and in-person transactions, meaning you only have to integrate once. No need to manage separate codebases or rebuild workflows when you expand into new channels.

Our developer support team works with you to review your implementation, optimize your workflows, and ensure everything is certified before launch.

You’ll also have access to SDKs and developer libraries across common languages, making it easy to plug payments directly into your existing platform. We’re pre-certified, pre-licensed, and pre-integrated with major payment terminals and networks, so if you wanted to accept in-person payments, you could do so without building new infrastructure. After launch, we handle ongoing maintenance, updates, and settlements so that you can stay focused on building your SaaS.

White-label payments and the freedom to set your own pricing

Fiska provides full white-label functionality across every checkout screen, receipt, onboarding form, and merchant dashboard. You design your user experience, and everything can be customized to fit your brand.

Behind the scenes, Fiska handles all backend compliance and payments risk, including PCI-DSS, KYC/KYB, AML, and fraud prevention.

Stripe Connect

stripe-connect-header

Stripe Connect is one of the most widely used embedded payment solutions for SaaS platforms seeking fast payment setup, and some of their well-known clients include Shopify, Zillow, and Uber.¹

Stripe Connect charges a flat 2.9% + $0.30 USD per online transaction, with no fixed monthly fee. In order to use Stripe Connect, all of your merchants need to have a Stripe account.

They provide pre-certified POS hardware, built-in tokenization, and global compliance coverage. The platform doesn’t have its own support system, and instead uses the same ticket-based infrastructure as Stripe’s main platform.

Stripe Connect offers multiple account types, but advanced customization options are only available through Custom or Express accounts. For example, using Stripe’s prebuilt components like Connect Onboarding allows you to launch payments faster, but fully white-labeled onboarding requires building your own onboarding UI. This is resource-intensive and recommended only for platforms with significant development capacity.

Finix

Finix is a Payfac-As-A-Service that serves a broad user base, including: software platforms, marketplace platforms, and individual businesses of all sizes.²

They offer both flat-rate and interchange-plus pricing, with varying rates depending on if you’re in the US or Canada. All their charges are transparently listed on their website.^2a

Finix’s platform supports omnichannel payments with built-in payment tokenization and pre-certified POS terminals.

It’s a white-label solution that includes embedded onboarding, reporting, and chargeback management. Independent Software Vendors (ISVs) can create custom fee profiles for merchants, applying volume-based discounts or transaction-specific pricing. However, setting up these configurations may require significant technical expertise since Finix’s API documentation is extensive.²

While Finix offers strong flexibility, it lacks industry-specific risk models for highly regulated verticals like healthcare or legal. As a result, ISVs may need to invest additional effort to customize Finix’s tools. Finix’s website also doesn’t mention having level 2 merchant support.²

Work with an embedded payments partner that supports you both technically and strategically

Choosing the right payment solution for your SaaS can feel overwhelming, especially when there’s such an exhausting amount of options out there. But if you’re setting up payments for the first time, then we believe that Fiska’s embedded payment solution is the best choice.

Our omnichannel API simplifies integration and lowers long-term maintenance costs. You’ll be supported by a dedicated team (both technically and strategically) so that you can go live in just a few weeks. Payments can be fully white-labeled, and our pricing is fully customizable.

Interested in working with Fiska? Book a no-obligation call with a member of our team to see how we can get you set up with payments.

FAQs:

1. How hard is it to integrate payments into my SaaS business?

Providers like Fiska simplify integration by using a single omnichannel API that supports both card-present and card-not-present transactions, meaning you only need to integrate once. This helps streamline your payment flows without building multiple checkout or payment gateway configurations.

2. How fast can I launch payments with Fiska?

Fiska allows SaaS platforms to launch online and in-person payments within a few weeks. Here’s what the onboarding lifecycle typically looks like:

Discovery Phase: We review your payment flows, recurring payment needs, CRM and reporting requirements, and how payments fit into your customer lifecycle.
Kickoff & Resource Allocation: We align on timelines, responsibilities, sandbox access, and API documentation.
Integration & Certification: Your developers integrate our unified API/SDKs for cards, ACH/EFT, and supported currencies (like USD and CAD). We provide real-time technical support and ensure any necessary certification for card-present payments is completed. We also help configure processor-level fraud prevention tools.
Launch Phase: We agree on a go-live date and begin merchant onboarding. Post-launch, we support you with payment data, reporting, and ongoing optimization as your platform scales.

3. What’s the best payment solution for SaaS?

The best payment solutions for SaaS are platforms built specifically for software companies, with strong support for recurring payments, onboarding, payouts, and automation.

SaaS-specific solutions like Fiska give platforms more control over their payments infrastructure and help create a more consistent, branded customer experience.

4. Should I become a PayFac as a SaaS platform?

Most SaaS businesses don’t become PayFacs because the cost, liability, and regulatory overhead outweigh the benefits: especially when managing recurring payments and revenue operations.

Instead of becoming a PayFac, many software teams choose:

Embedded payments
PayFac-as-a-Service
SaaS-focused payment processing providers

These routes offer better scalability and monetization without taking on full compliance and underwriting responsibilities.

5. How do I earn revenue from payments as a software company?

When you embed payments, every transaction becomes a new revenue line. SaaS platforms typically monetize payments through:

Custom markups
Revenue share
Offering enhanced payment features such as recurring payment tools, integrated invoicing options, and smoother merchant onboarding flows

6. Does Fiska support multi-currency payments?

Yes. Fiska supports payments in USD, CAD, and additional currencies depending on region and acquiring arrangements.

This is ideal for SaaS startups serving customers across borders or those preparing to expand into new markets with global payment capabilities.

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