Best Payment Gateways for SaaS Companies

For SaaS companies seeking to efficiently embed payments, scale operations, and maintain full control over their payment ecosystem, Finix offers a flexible, reliable, and developer-friendly solution that combines compliance, risk management, and monetization capabilities in a single platform.

In the SaaS economy of 2025, where subscription-based models dominate, the choice of a payment gateway is more than a technical decision; it’s a strategic lever. For software-as-a-service (SaaS) platforms, embedding payments rather than redirecting customers to external checkout pages can significantly increase retention, generate new revenue streams, and deepen the brand relationship.

Not every payment provider is built the same. SaaS companies have specific needs, including recurring billing, flexible fee structures, risk management, and fraud protection, among others. In this post, we’ll explore why embedded payments are critical for SaaS, survey the top payment gateways for this use case, and show why Finix stands out as a best-in-class choice.

Why Embedded Payments Matter for SaaSCopy to clipboard

1. Better Customer Experience

When payments are embedded directly into the SaaS product (rather than sent off to a third-party checkout), users enjoy a cleaner, more seamless experience. According to Finix’s embedded payments guide, removing redirects and third-party handoffs reduces friction and reinforces a cohesive in-app flow.

2. Stronger Retention & Stickiness

Embedded payments integrate financial interactions into the product itself, helping to lock in customers. As Finix points out, this setup supports predictable revenue, simplifies billing, and gives the SaaS provider real-time visibility into transaction flows.

3. New Monetization Opportunities

For SaaS platforms, payments aren’t just about processing. Embedded payments offer platforms a way to monetize by charging transaction fees, sharing revenue, or providing value-added features such as instant payouts or premium cash flow management.

4. Operational Efficiency

Handling payments in-house (or semi-in-house) reduces reliance on multiple providers. It centralizes reconciliation, underwriting, reporting, and risk control into a single dashboard. This is especially impactful for scaling businesses.

How SaaS Companies Implement Embedded PaymentsCopy to clipboard

SaaS firms generally take one of two paths to embed payments:

1. Become a PayFac (Payment Facilitator)

   • The company becomes a registered payment facilitator (PayFac), underwrites its own sub-merchants, assumes KYC and risk responsibilities, and directly disburses payouts.

   • Pros: Maximum control, potential for higher margins, full ownership of the payments business.

   • Cons: Heavy regulatory burden, resource-intensive, requires building infrastructure, and potentially millions in investment.

2. Use PayFac-as-a-Service (PFaaS)

   • Instead of doing everything in-house, the SaaS company partners with a provider that offers payment infrastructure and compliance-as-a-service.

   • Pros: Faster time-to-market, lower regulatory risk, less technical overhead.

   • Cons: Some trade-off in control, but for many SaaS companies, this is the sweet spot.

Finix supports both models, giving SaaS platforms the flexibility to adapt based on their scale, ambition, and risk appetite.

Key Criteria for Evaluating Payment Gateways for SaaSCopy to clipboard

When evaluating payment gateways for SaaS, companies should prioritize:

• Recurring Billing & Subscription Support: Ability to build flexible subscription plans, smart retry logic, trial periods, and more.

• Developer Experience: API reliability, documentation, and integration flexibility.

• Ownership of the Payment Flow: Custom branding, white-labeled onboarding, and dashboard capabilities.

• Risk & Compliance Tools: Underwriting, fraud detection, dispute management.

• Reporting & Transparency: Detailed, real-time dashboards, reconciliation, and granular transaction-level data.

• Scalability & Uptime: Infrastructure reliability, failover systems, and the ability to scale as volume grows.

• Cost Structure: Custom fee profiles, payout settings, and ways to monetize payments.

Why Finix Is the Best Payment Gateway for SaaS CompaniesCopy to clipboard

Here are the key reasons why Finix is particularly well-suited for SaaS companies, backed by real, citable data.

1. Designed Specifically for Software Platforms

On its “Who We Serve” page, Finix emphasizes that it is purpose-built for software platforms. Finix delivers “PayFac-as-a-Service” with end-to-end payments infrastructure, compliance, and risk management. That means SaaS platforms can benefit from payments without having to become full-fledged payment institutions from day one.

2. High Reliability & Scalability

Finix’s API-driven layer is built to handle massive scale. According to their site, it handles billions of API calls per year with 99.999% uptime. This level of reliability is critical for SaaS companies running mission-critical platforms.

3. Deep Reporting & Operational Transparency

Finix offers more than 10 out-of-the-box report types, including transaction-level data, interchange, reconciliation, settlements, disputes, and fees. This helps SaaS platforms maintain control and visibility over their payments business.

They also provide each sub-merchant (i.e., the SaaS customer’s customers) with a white-labeled merchant dashboard, allowing your users to monitor their own transactions, disputes, and payouts all under your brand.

4. Flexible Fee Structures & Payout Settings

With Finix, SaaS companies can define custom fee profiles per merchant or per transaction. That means you can structure pricing to maximize margins, pass through costs, or optimize for specific high-value customers. Payout settings are also configurable, giving your business flexibility over how and when funds are disbursed.

5. Fraud Prevention & Dispute Management

Finix includes fraud monitoring by default, helping detect suspicious activity before chargebacks happen. And when disputes do arise, their dashboard supports dispute-tracking. This is especially valuable for SaaS businesses that want to minimize risk while maintaining a smooth payment experience.

6. Developer-Friendly with No-Code / Low-Code Options

While Finix’s API is rich and configurable, with “hundreds of API configurations,” they’ve also recently released a suite of no-code/low-code tools designed to speed up payment integration for non-technical teams. In July 2024, they launched:

• Checkout Pages

• Payment Links

• Tokenization Forms

• Virtual Terminals

• Merchant Onboarding Forms

This helps SaaS companies that don’t have large engineering teams or want to move fast without sacrificing control.

7. Recurring Billing Built for Subscriptions

In July 2024, Finix introduced a Recurring Billing solution on its dashboard, allowing users to create and manage subscription plans without code. The Global Newswire Features include trial periods, smart retry logic, account updater, and network tokens,  all crucial tools for SaaS platforms that run on recurring revenue.

8. High Growth & Financial Strength

Finix has raised significant capital: in October 2024, it closed $75 million in funding to boost the adoption of its payment platform and scale its business. This demonstrates investor confidence and the financial resources required to support a growing, scalable payments infrastructure.

Risks & Considerations for SaaS PlatformsCopy to clipboard

While Finix is compelling, SaaS founders need to reflect on a few trade-offs and challenges:

1. Onboarding & Underwriting Even though Finix streamlines underwriting, there are still processes for merchant onboarding, KYC, and risk assessment. For specific verticals (high-risk, regulated), this may require additional operational effort.

2. Commitment to Platform Strategy Embedding payments means integrating payments into your product. That bears both opportunity and responsibility. Your product, engineering, and compliance teams must align to maintain uptime, reconcile payments, and resolve disputes.

3. Cost Structure While Finix provides flexible fee profiles, SaaS companies must carefully model how they will charge their customers. Whether you absorb payment costs, pass them through, or add a margin, there is a delicate balancing act between customer competitiveness and profitability.

4. Scaling Risk As transaction volume increases, so do risks (fraud, chargebacks). Even with fraud tools, scaling payments means investing in operations.

Best Practices for SaaS Companies Implementing Embedded Payments with FinixCopy to clipboard

To get the most out of Finix (or any embedded payments partner), SaaS companies should follow these best practices:

1. Start with a Minimal Viable Integration Use Finix’s no-code or low-code tools (checkout pages, payment links) to test your payment flows early. This can accelerate time-to-value without an enormous dev burden.

2. Design for Recurring Billing From Day One Leverage Finix’s Recurring Billing to set up trial periods, retry logic, and account updater. This reduces churn and automates billing.

3. Brand Everything Use white-labeled onboarding and dashboards so your users never feel like they left your platform. Finix’s embedded dashboards support this.

4. Implement Strong Webhook Handling Build your backend to handle webhooks (payment succeeded, failed, or refunded) in real-time, so your UI stays in sync and edge cases are handled gracefully.

5. Monitor Risk & Fraud Proactively Use Finix’s built-in fraud monitoring. Set up alerts and custom rules for your business patterns.

6. Leverage Reporting Dive into transaction-level, reconciliation, and payout reports. Use them to optimize margins, identify pain points, and forecast cash flow.

Selecting the right payment gateway is a foundational decision for SaaS companies. More than just processing transactions, the ideal partner can influence customer experience, retention, revenue models, and long-term scalability.

Finix stands out in this landscape. Its deep focus on software platforms, robust and reliable APIs, no-code/low-code toolset, robust reporting, and support for both PayFac-as-a-Service and full payments ownership make it uniquely suited for SaaS companies that want full control over their payment flow, without the multi-year, multimillion-dollar lift of building from scratch.

For SaaS founders serious about embedding payments in a way that is seamless, scalable, and monetizable, Finix is one of the strongest contenders.

Ready to see what embedded payments could look like inside your platform? Connect with Finix and explore how fast you can launch.