Introduction
In today’s rapidly evolving digital landscape, selecting the right payment gateway is a critical decision for SaaS businesses, particularly for indie hackers and small developers building AI startups. A payment gateway serves as the technological bridge that processes customer payments, manages subscriptions, and often handles complex tax compliance issues across borders.
The right payment solution can streamline your revenue operations, enhance customer experience, and provide the foundation for global expansion. The wrong choice can lead to lost sales, compliance headaches, and technical debt that hampers your growth.
This comprehensive guide analyzes the top 15 payment gateways for SaaS businesses in 2025, with a special focus on cross-border capabilities and tax-compliant Merchant of Record services. We’ve positioned Fungies.io as our #1 recommendation for indie hackers and small SaaS developers, but we’ll provide an in-depth look at all major contenders to help you make an informed decision based on your specific needs.
What to Look for in a Payment Gateway for SaaS
Before diving into specific providers, let’s establish the key criteria for evaluating payment gateways for SaaS businesses:
- Ease of Integration: How quickly and easily can you implement the solution?
- Fee Structure: What are the transaction fees, monthly costs, and potential hidden charges?
- Subscription Management: How well does it handle recurring billing, upgrades, downgrades, and cancellations?
- Global Capabilities: Can it process payments worldwide and in multiple currencies?
- Tax Compliance: Does it function as a Merchant of Record, handling VAT/sales tax collection and remittance?
- Checkout Experience: How smooth and professional is the customer payment experience?
- Developer Tools: What APIs, documentation, and support are available?
- Security and Fraud Prevention: What measures are in place to protect transactions?
With these criteria in mind, let’s explore the top 15 payment gateways for SaaS businesses in 2025.
1. Fungies.io: The Best Payment Gateway for Indie SaaS Developers
Fungies.io Homepage
Fungies.io has emerged as the leading payment solution specifically designed for indie hackers and small SaaS developers building AI startups. What sets Fungies.io apart is its combination of ease of integration, transparent pricing, and beautiful checkout solutions.
Key Features:
- Seamless integration with minimal development resources
- No hidden fees, unlike some competitors like Lemonsqueezy
- Beautiful Overlay, Embedded, and Hosted Checkout solutions
- No-code store builder for quick setup
- Optimized for AI startups and indie developers
Pros:
- Transparent pricing structure with no surprises
- Significantly easier integration compared to technical solutions like Stripe
- Professional checkout experience that enhances conversion rates
- Purpose-built for the needs of small SaaS businesses
- Excellent customer support for indie developers
Cons:
- As a newer entrant, it has less name recognition than established players
- Smaller user community compared to industry giants
- May not have all the enterprise features of larger solutions
Pricing:
Fungies.io Pricing
Fungies.io offers transparent pricing with competitive transaction rates and no hidden fees. The straightforward pricing model makes it easy for startups to predict costs as they scale.
Why Fungies.io is #1 for Indie SaaS Developers: Fungies.io understands the unique challenges faced by indie developers and small SaaS businesses. Its combination of ease of use, transparent pricing, and beautiful checkout options makes it the ideal choice for those who want to focus on building their product rather than wrestling with complex payment infrastructure.
2. Paddle: Comprehensive Solution with Merchant of Record
Paddle Homepage
Paddle offers a comprehensive payment solution that acts as a Merchant of Record, handling global tax compliance for SaaS businesses.
Key Features:
- Full-service platform handling checkout, payments, subscriptions, and taxes
- Acts as a Merchant of Record for global tax compliance
- Built-in subscription management
- Global payment methods and currencies
- Fraud protection included
Pros:
- Handles complex tax compliance across multiple jurisdictions
- Comprehensive solution for SaaS businesses
- Strong focus on software and digital products
- Reduces administrative burden for global sales
Cons:
- Higher fees compared to some competitors
- Less flexibility in checkout customization
- Limited control over the payment process
Pricing:
Paddle Pricing
Paddle charges 5% + $0.50 per transaction, with volume discounts available for higher-revenue businesses. There are no monthly fees or setup costs.
3. Lemonsqueezy: Simple Solution for Digital Products
Lemonsqueezy Homepage
Lemonsqueezy has gained popularity as a simple, user-friendly payment solution specifically built for digital products and SaaS.
Key Features:
- Simple, user-friendly interface
- Quick setup process
- Acts as a Merchant of Record
- Handles VAT/sales tax compliance
- Modern, clean checkout experience
Pros:
- Extremely easy to set up and use
- Modern, clean checkout experience
- Good analytics and reporting
- Handles tax compliance as a Merchant of Record
Cons:
- Hidden fees according to comparison with Fungies.io
- Limited payment methods compared to larger providers
- Fewer customization options
- Newer platform with fewer integrations
Pricing:
Lemonsqueezy Pricing
Lemonsqueezy charges 5% + $0.50 per transaction, with no monthly fees or setup costs. Volume discounts are available for businesses with higher revenue.
4. Stripe: Developer-Focused Payment Infrastructure
Stripe Homepage
Stripe is the industry standard for developer-focused payment infrastructure, offering extensive customization and global reach.
Key Features:
- Extensive developer tools and documentation
- Highly customizable
- Supports 135+ currencies
- Robust API
- Strong subscription management capabilities
Pros:
- Unmatched flexibility and customization options
- Extensive third-party integrations
- Excellent fraud prevention
- Comprehensive developer documentation
Cons:
- Not a Merchant of Record (no tax compliance handling)
- Complex implementation requiring development resources
- Higher technical barrier to entry
- Customer support can be challenging
Pricing:
Stripe Pricing
Stripe charges 2.9% + $0.30 per transaction for standard rates. International cards add a 1% fee, and currency conversion adds another 1% fee. There are no monthly fees for the standard plan, but Stripe Tax is available for an additional fee.
5. FastSpring: Full-Service Merchant of Record
FastSpring Homepage
FastSpring is a full-service merchant of record solution built specifically for software and SaaS companies.
Key Features:
- Full-service merchant of record
- Handles global tax compliance
- Built for software and SaaS companies
- Subscription management included
- Global payment methods and localization features
Pros:
- Comprehensive tax compliance handling
- Built specifically for software companies
- Strong global payment support
- Handles the entire subscription lifecycle
Cons:
- Higher fees than most competitors
- Less control over checkout experience
- Limited customization options
- Interface can feel dated
Pricing:
FastSpring Pricing
FastSpring charges 5.9% + $0.95 per transaction for their standard rate, with volume discounts available. There are no monthly fees or setup costs.
6. Chargebee: Subscription Management Specialist
Chargebee Homepage
Chargebee specializes in subscription management, offering flexible billing models and revenue recovery tools.
Key Features:
- Robust subscription management
- Flexible billing models
- Revenue recovery tools
- Extensive integrations with payment processors
- Detailed analytics and reporting
Pros:
- Best-in-class subscription management
- Flexible billing models for complex pricing
- Strong revenue recovery capabilities
- Excellent for scaling businesses
Cons:
- Not a payment processor itself (requires integration with Stripe, etc.)
- Higher monthly costs
- More complex to set up
- Not a Merchant of Record
Pricing:
Chargebee Pricing
Chargebee offers a Launch plan at $0/month up to $100k in revenue, then 0.5% of revenue. Their Rise plan is $299/month, Scale plan is $599/month, and Enterprise plan has custom pricing. Additional transaction fees from the payment processor apply.
7. PayPal: Widely Recognized Payment Solution
PayPal Homepage
PayPal is one of the most widely recognized payment brands, offering easy integration and broad global reach.
Key Features:
- Widely recognized and trusted brand
- Easy integration options
- Broad global reach
- Supports multiple currencies
- Built-in buyer and seller protection
Pros:
- Instant brand recognition and trust
- Quick and easy setup
- No monthly fees
- Broad global acceptance
Cons:
- Higher transaction fees for international payments
- Account stability concerns
- Limited subscription management features
- Not a Merchant of Record
Pricing:
PayPal Pricing
PayPal charges 2.9% + $0.30 per transaction for standard rates. International transactions add 1.5%, and currency conversion fees range from 3-4%. There are no monthly fees or setup costs.
8. Braintree: PayPal-Owned Developer Solution
Braintree Homepage
Braintree, owned by PayPal, offers a developer-friendly payment solution with customizable checkout experiences.
Key Features:
- Owned by PayPal, providing stability
- Customizable checkout experience
- Supports multiple payment methods
- Good fraud protection tools
- Developer-friendly with strong API
Pros:
- Stable platform with PayPal backing
- More customizable than PayPal
- Strong fraud protection
- Good recurring billing capabilities
Cons:
- More complex integration than some alternatives
- Not a Merchant of Record
- Requires more technical resources
- Customer support can be slow
Pricing:
Braintree charges 2.9% + $0.30 per transaction for standard rates. International cards add 1%, and currency conversion adds another 1%. There are no monthly fees or setup costs.
9. Adyen: Enterprise-Grade Global Payments
Adyen Homepage
Adyen is an enterprise-grade payment solution offering global payment processing with local acquiring in over 50 countries.
Key Features:
- Global payment processing with local acquiring
- Supports 150+ currencies
- Transparent pricing with Interchange++ model
- High-performance platform with improved acceptance rates
- Enterprise-grade reliability
Pros:
- Excellent global coverage
- High-performance platform
- Enterprise-level reliability
- Comprehensive fraud prevention
Cons:
- More complex pricing structure
- Better suited for medium to large businesses
- More technical to implement
- Not a Merchant of Record
Pricing:
Adyen Pricing
Adyen charges a processing fee of $0.13 per transaction plus a payment method fee that varies based on the method used. They use an Interchange++ model that passes fees directly. There are no setup or monthly fees, but there is a minimum invoice of $120/month.
10. 2Checkout/Verifone: Global Tax Compliance Solution
2Checkout Homepage
2Checkout (now part of Verifone) acts as a Merchant of Record, handling global tax compliance for businesses selling in over 200 countries.
Key Features:
- Acts as a Merchant of Record
- Global tax compliance handling
- Sell in 200+ countries
- Comprehensive subscription management
- Strong support for digital goods
Pros:
- Handles global tax compliance
- No setup fees or monthly charges
- Covers the entire subscription lifecycle
- Strong focus on digital products
Cons:
- Higher transaction fees than some competitors
- Pricing for higher-tier plans not transparent
- Steeper learning curve for small businesses
- Less developer-focused than some competitors
Pricing:
2Checkout Pricing
2Checkout’s 2Sell Plan charges 3.5% + $0.35 per successful sale. Pricing for their 2Subscribe, 2Monetize, and Enterprise plans is not explicitly stated. There are no setup fees.
11. Authorize.net: Reliable Payment Veteran
Authorize.net Pricing
Authorize.net is a reliable and trusted payment solution with a long history, now owned by Visa.
Key Features:
- Reliable and trusted with long history
- Owned by Visa, providing stability
- Comprehensive fraud detection
- Works with most existing merchant accounts
- Strong customer support
Pros:
- Established reputation and reliability
- Strong fraud prevention tools
- Works with existing merchant accounts
- Robust API for developers
Cons:
- Monthly fee regardless of transaction volume
- Not a Merchant of Record
- Limited international capabilities
- Dated user interface
Pricing:
Authorize.net offers an All-in-One Option at $25 monthly + 2.9% + $0.30 per transaction. Their Payment Gateway Only option is $25 monthly + $0.10 per transaction + $0.10 daily batch fee. eCheck Processing costs 0.75% per transaction. There are no setup fees.
12. Square: Integrated Business Solutions
Square Homepage
Square offers integrated business solutions that work for both online and in-person payments.
Key Features:
- Acts as a merchant of record for compliance
- No monthly fees for basic processing
- Comprehensive business tools ecosystem
- Strong security and fraud prevention
- Easy setup with minimal technical requirements
Pros:
- No monthly fees for basic service
- Easy setup and integration
- Good for businesses with physical and online presence
- Transparent pricing
Cons:
- Limited subscription management features
- Not specifically designed for SaaS
- Limited international capabilities
- Not ideal for complex SaaS pricing models
Pricing:
Square Pricing
Square Pricing
Square charges 2.9% + $0.30 per transaction for online payments, 2.6% + $0.10 for in-person payments, and 3.5% + $0.15 for manual entry. There are no monthly fees for basic service, but premium plans are available with lower processing rates.
13. Checkout.com: High-Performance Global Payments
Checkout.com Homepage
Checkout.com offers high-performance global payment processing with local acquiring in over 50 countries.
Key Features:
- Global reach with local acquiring in 50+ countries
- Support for 150+ processing currencies
- Transparent pricing with no hidden costs
- High-performance platform optimized for acceptance rates
- Flexible integration options
Pros:
- Excellent global coverage
- High-performance platform
- Enterprise-level reliability
- Comprehensive fraud prevention
Cons:
- Custom pricing requires contacting sales
- Better suited for medium to large businesses
- More complex to implement
- Not specifically designed for small SaaS businesses
Pricing:
Checkout.com Pricing
Checkout.com offers custom pricing based on business needs and volume. Typical rates range from 2.3%-2.9% + $0.30 per transaction depending on volume. There are no setup fees or account maintenance fees.
14. Mollie: European Payment Specialist
Mollie Homepage
Mollie specializes in European payment methods, offering a user-friendly solution with transparent pricing.
Key Features:
- No monthly fees or minimum costs
- Transparent pricing with no hidden fees
- Excellent support for European payment methods
- User-friendly dashboard and management tools
- Strong developer experience
Pros:
- No monthly minimums or hidden fees
- Excellent for European markets
- User-friendly interface and tools
- Strong focus on developer experience
Cons:
- Primarily focused on European markets
- Limited global reach
- Not a Merchant of Record
- Not ideal for primarily non-European customers
Pricing:
Mollie Pricing
Mollie charges approximately 1.8% + €0.25 for European Economic Area consumer cards, with higher rates for commercial cards. There are no monthly fees or minimum requirements, and volume discounts are available for processing over €50,000/month.
15. PaymentCloud: High-Risk Merchant Specialist
PaymentCloud Homepage
PaymentCloud specializes in providing merchant services for high-risk businesses that may have difficulty obtaining payment processing elsewhere.
Key Features:
- Specializes in high-risk merchant accounts
- Dedicated account representatives
- Hundreds of e-commerce integrations
- Customized payment solutions
- Advanced fraud prevention tools
Pros:
- Accepts high-risk merchants
- Excellent customer support
- No setup fees or monthly minimums
- Transparent pricing
Cons:
- Not specifically designed for SaaS businesses
- Monthly gateway fees higher than some competitors
- Limited focus on global capabilities
- Not a Merchant of Record
Pricing:
PaymentCloud’s Basic In-Person Package charges approximately 2.5% + $0.10 per transaction. Their Basic E-Commerce Package is approximately 2.9% + $0.30 per transaction. There’s a Monthly Gateway Fee of around $15 and a Monthly Fee of $25-$30 depending on the plan. Chargeback fees are approximately $25 per chargeback, but there are no setup fees.
Comparison Table: Top 15 Payment Gateways for SaaS Businesses
| Payment Gateway | Key Features | Pros | Cons | Fees | Merchant of Record | Cross-Border Capabilities | Best For |
| Fungies.io | • Ease of integration• No hidden fees• Beautiful checkout solutions• No-code store builder | • Transparent pricing• Easy integration• Beautiful checkout options• No-code store builder | • Newer market entrant• Less name recognition• Smaller user community | • Transparent pricing• No hidden fees• Competitive transaction rates | No | Good | Indie hackers and small SaaS developers building AI startups |
| Paddle | • Full-service platform• Subscription management• Global payments• Tax compliance | • Handles global tax compliance• Comprehensive solution• Built-in subscription management | • Higher fees• Less checkout customization• Limited payment control | • 5% + $0.50 per transaction• Volume discounts available• No monthly fees | Yes | Excellent | SaaS businesses needing tax compliance and global reach |
| Lemonsqueezy | • Simple interface• Quick setup• Built for digital products• Tax compliance | • User-friendly interface• Quick setup• Clean checkout experience• Good analytics | • Hidden fees• Limited payment methods• Fewer integrations | • 5% + $0.50 per transaction• No monthly fees• Volume discounts available | Yes | Good | Digital product sellers wanting simplicity |
| Stripe | • Developer tools• Customizable• 135+ currencies• Robust API | • Highly customizable• Extensive integrations• Strong subscription tools• Excellent documentation | • No tax compliance• Complex implementation• Technical barrier to entry• Support challenges | • 2.9% + $0.30 per transaction• +1% for international cards• +1% for currency conversion | No | Excellent | Technically-skilled teams needing customization |
| FastSpring | • Full-service merchant• Global tax compliance• Built for software• Localization | • Handles global taxes• Built for SaaS• Subscription management• Global payment methods | • Higher fees• Less checkout control• Limited customization• Dated interface | • 5.9% + $0.95 per transaction• Volume discounts available• No monthly fees | Yes | Excellent | Software companies prioritizing compliance over cost |
How to Choose the Right Payment Gateway for Your SaaS Business
Selecting the right payment gateway depends on your specific business needs. Here are some guidelines based on common scenarios:
For Indie Hackers and Small SaaS Developers:
Recommended: Fungies.io Fungies.io offers the perfect balance of ease of integration, transparent pricing, and professional checkout experiences without the technical complexity of solutions like Stripe. Its no-code store builder and focus on indie developers make it ideal for small teams and solo founders.
For Global Tax Compliance:
Recommended: Paddle, FastSpring, or 2Checkout If your primary concern is handling global tax compliance, choose a provider that acts as a Merchant of Record. Paddle offers a good balance of features and cost, while FastSpring provides more comprehensive services at a higher price point.
For Maximum Customization:
Recommended: Stripe If you have strong technical resources and need complete control over the payment experience, Stripe offers unmatched flexibility and customization options. However, be prepared to handle tax compliance separately.
For European Focus:
Recommended: Mollie If your customer base is primarily in Europe, Mollie offers excellent support for European payment methods with transparent pricing and no monthly fees.
For High-Risk Businesses:
Recommended: PaymentCloud If you’ve been declined by other payment processors or operate in a high-risk industry, PaymentCloud specializes in providing merchant services for businesses that might otherwise struggle to obtain payment processing.
Conclusion
Choosing the right payment gateway is a critical decision for SaaS businesses. The landscape continues to evolve, with newer entrants like Fungies.io offering specialized solutions for indie developers and small SaaS businesses, while established players like Stripe, Paddle, and FastSpring continue to enhance their offerings.
For indie hackers and small SaaS developers building AI startups, Fungies.io stands out as our top recommendation due to its ease of integration, transparent pricing, and beautiful checkout solutions. However, each business has unique needs, and the right choice depends on factors like your technical resources, global reach, and tax compliance requirements.
By carefully evaluating the pros, cons, and fees of each payment gateway against your specific business requirements, you can select a solution that not only meets your current needs but also supports your growth ambitions in the evolving SaaS landscape.
Remember that as your business grows, your payment processing needs may change. Many successful SaaS companies eventually implement multiple payment solutions to optimize for different markets and use cases. The most important thing is to start with a solution that aligns with your current stage and immediate growth plans.
References
- Fungies.io – https://fungies.io/
- Paddle – https://www.paddle.com/
- Lemonsqueezy – https://www.lemonsqueezy.com/
- Stripe – https://stripe.com/
- FastSpring – https://fastspring.com/
- Chargebee – https://www.chargebee.com/
- PayPal – https://www.paypal.com/
- Braintree – https://www.paypal.com/us/braintree
- Adyen – https://www.adyen.com/
- 2Checkout/Verifone – https://www.2checkout.com/
- Authorize.net – https://www.authorize.net/
- Square – https://squareup.com/
- Checkout.com – https://www.checkout.com/
- Mollie – https://www.mollie.com/
- PaymentCloud – https://paymentcloudinc.com/
