7 Best Payment Gateways for SaaS Applications

With a focus on subscription management, global payments, and security features.

Payment Gateways Payments SaaS Subscription Management Global Payments Online Transactions Billing Digital Payments Security Stripe PayPal Braintree 2checkout

14 January 2025

Choosing the right payment gateway can be tricky for SaaS businesses. Here’s a quick summary of the top 7 payment gateways tailored for SaaS needs, focusing on subscription management, global payments, security, and pricing.

The 7 Best Payment Gateways:

Stripe: Advanced subscription tools, global reach (130+ currencies), and smart retries for failed payments.
- Fees: 2.9% + $0.30 per domestic transaction.
PayPal: Trusted globally with flexible billing models and analytics.
- Fees: 3.49% + $0.49 for domestic transactions.
Braintree: Owned by PayPal, supports prorated billing and secure card storage.
- Fees: 2.59% + $0.49 per transaction.
Authorize.Net: Offers automated recurring billing and strong security.
- Fees: $25/month + 2.9% + $0.30 per transaction.
Square: Easy-to-use tools for recurring invoicing and secure card storage.
- Fees: 2.9% + $0.30 for online transactions.
2Checkout: Owned by Verifone. Great for global SaaS businesses with advanced retry logic.
- Fees: 3.5% + $0.35 for basic plans.
GoCardless: Specializes in direct bank payments with low transaction costs.
- Fees: 0.5% + $0.05 per transaction.

Quick Comparison Table

Gateway	Monthly Fee	Domestic Fee	Global Support	Subscription Features
Stripe	$0	2.9% + $0.30	130+ currencies	Smart retries, usage-based billing
PayPal	$0–$30	3.49% + $0.49	100+ currencies	Flexible billing, analytics
Braintree	$49	2.59% + $0.49	130+ currencies	Prorated billing, fraud protection
Authorize.Net	$25	2.9% + $0.30	12+ currencies	Recurring billing, eCheck
Square	$0	2.9% + $0.30	5+ currencies	Recurring invoicing, reminders
2Checkout	$0	3.5% + $0.35	100+ currencies	Retry logic, tax handling
GoCardless	$0	0.5% + $0.05	30+ countries	Direct debit, intelligent retries

Each gateway has unique strengths, so the best choice depends on your business size, global reach, and subscription needs. Read on for detailed features and pricing!

The 7 Best Payment Gateways for Small Business

1. Stripe

Stripe stands out as a top payment gateway for SaaS businesses, offering tools like Stripe Billing to simplify subscription management. It’s a go-to choice for companies aiming to grow and streamline their operations.

Key Features for SaaS

Stripe’s subscription management system accommodates various billing models, including:

Usage-based pricing
Tiered pricing structures
Flat fees with overage charges
Custom pricing for enterprise clients

One standout feature is Smart Retries, which helps recover an average of 57% of failed recurring payments. In 2023, Stripe’s recovery tools helped businesses reclaim over $3.4 billion in revenue.

Pricing Overview

Stripe’s pricing includes:

Standard fees: 2.9% + $0.30 per domestic transaction
Additional 1.5% for international cards
1% for currency conversion
Stripe Billing: 0.7% of billing volume (pay-as-you-go) or starting at $620 per month with an annual contract

Integration and Management Tools

Stripe offers a self-service customer portal that allows subscribers to:

Manage subscriptions
Update payment details
View invoice history
Adjust plans with automatic prorating

”Scaling our products means giving our users flexible subscription options. With Stripe Billing, we quickly rolled out monthly pay-as-you-go options for ChatGPT and our API, respectively.” - OpenAI

Stripe also excels in scaling globally and ensuring security.

Global Reach and Security Features

Stripe supports over 40 local payment methods and 130+ currencies. It includes automated tax calculation, compliance features, and built-in PCI DSS compliance. Additionally, its machine learning-powered systems optimize revenue retention by timing retries and updating card details automatically.

”With billing, tax, reporting, and more on the same platform, Stripe automation helps eliminate inefficient processes as we scale the business. And that’s essential as we continue supporting Retool’s growth with a relatively small team.” - Retool

Feature	Details
Transaction Processing	2.9% + $0.30 per domestic charge
Subscription Management	Built-in billing tools
Global Coverage	130+ currencies, 40+ payment methods
Integration Options	API, no-code solutions, webhooks

While Stripe’s fees can be higher than some competitors - SaaS founders report costs ranging from 4-8% of revenue - its reliability and extensive features make it a strong choice for businesses focused on growth and automation.

2. PayPal

PayPal is a popular choice for SaaS companies, offering tools for managing recurring billing and handling global transactions. While Stripe focuses on technical integration, PayPal stands out for its broad user trust and extensive global network, making it ideal for businesses looking to maximize payment acceptance.

Key SaaS Features

PayPal’s subscription tools include:

Flexible billing models (fixed, quantity-based, and tiered pricing)
Automated retries for failed payments
Real-time analytics dashboard
Options for customizable trial periods and promotional offers
Support for multiple currencies in international billing

Subscription Management Tools

PayPal simplifies recurring payment management with tools to automate billing communication and track performance metrics. These features help businesses smoothly transition from acquiring customers to managing ongoing revenue streams.

”By using PayPal subscription payments, it’s much easier for our users to renew and keep using the product, which improves our Lifetime Value (LTV).” - Gal Dubinski, Co-founder, Premio

Pricing Structure

Transaction Type	Fee Structure
Domestic	3.49% + $0.49
International	Standard fee + 1.50%
PayPal Payments Pro	$30 monthly
Payflow Pro	$25 monthly
Payflow Link	No monthly fee

Integration Options

PayPal offers several integration methods for SaaS platforms:

REST API for modern applications
Custom checkout forms
Instant Payment Notification (IPN) system
HTML payment buttons for quick setup

Security and Support

PayPal ensures secure transactions with fraud protection, SSL-encrypted payment processing, automated chargeback handling, and 24/7 customer support.

A recent survey found that 81% of PayPal users view it as an easy-to-use payment method. This ease of use, combined with support for over 100 currencies, makes it a strong option for SaaS companies prioritizing user experience. However, international transactions incur an additional 1.50% fee.

For businesses needing advanced features, the Commerce Platform for Marketplaces offers tools for complex billing scenarios. While it requires separate approval, it includes options like automated billing for outstanding balances, helping to streamline revenue collection and reduce manual work.

Although PayPal’s fees are slightly higher than some competitors, its global reach and extensive feature set make it a great fit for SaaS companies looking for simplicity and broad market appeal.

3. Braintree

Braintree, owned by PayPal, offers a platform designed to handle SaaS payments and subscription management. It focuses on simplifying recurring billing and managing subscription changes.

Key Features

Adjusts subscriptions automatically for plan changes (prorated billing).
Stores payment details securely in the Braintree Vault.
Updates card information automatically to reduce failed payments.
Provides real-time subscription status updates via webhooks.
Allows custom pricing with add-ons and promotional options.

Pricing Structure

Transaction Type	Standard Rate
Credit/Debit Cards	2.59% + $0.49
ACH Direct Debit	0.75% (max $5)
International Cards	3.59% + $0.49
Non-USD Currency	Additional 1%
Chargebacks	$15 per incident

Merchants processing over $80,000 monthly can negotiate custom interchange-plus rates. Payment expert Matt Rej cautions, “Do NOT accept these rates!”

Integration Options

Braintree supports two integration paths: the Drop-in UI for quick setup and the Custom UI for a more tailored checkout experience. It’s compatible with multiple programming languages, including Ruby, Python, PHP, Java, .NET, and Node.js. A basic integration can be completed in under 30 minutes, making it a good choice for fast-paced SaaS businesses. Beyond flexibility, Braintree prioritizes security across its platform.

Security and Compliance

Braintree meets Level 1 PCI DSS compliance and includes fraud protection at no additional cost. Key security features include:

Automated fraud detection.
Secure storage in a vault.
Device data collection.
Real-time transaction monitoring.

These measures make it a strong option for businesses requiring enterprise-level security.

Enterprise Scalability

Braintree integrates seamlessly with platforms like Salesforce, Adobe Commerce, Demandware, BigCommerce, and Magento, streamlining payment processes for both web and mobile applications.

However, its TrustPilot rating of 1.2 stars - primarily due to customer service issues - might be a concern for potential users.

4. Authorize.Net

Authorize.Net is a well-established payment solution offering tools tailored for managing SaaS subscriptions.

Key Features and Subscription Management

Authorize.Net’s Automated Recurring Billing (ARB) system handles payments via credit cards and bank accounts (eCheck). The Customer Information Manager (CIM) securely stores customer profiles, while the Account Updater automatically refreshes stored card details, minimizing failed transactions and reducing churn.

Some standout subscription features include:

Flexible billing schedules to accommodate various subscription models
Support for trial periods
An online portal for tracking subscriptions
API access for creating custom payment forms
PCI-DSS compliant payment storage

Pricing Structure

Plan Type	Monthly Fee	Transaction Fee	Additional Costs
All-in-One Processing	$25	2.9% + $0.30	Chargeback Fee: $25
Gateway-Only	$25	$0.10 per transaction	Daily Batch Fee: $0.10

For SaaS businesses processing over $500,000 annually, custom enterprise pricing is available.

Security Features

The CIM ensures secure customer profile storage, improving security while maintaining PCI compliance.

Integration Options

Authorize.Net supports API-first customization, offering multiple integration paths. While this flexibility is beneficial, advanced customization may require additional development resources. This aligns well with the needs of SaaS developers seeking scalable and adaptable payment solutions.

Cost Comparison

Although its pricing may be on the higher side, Authorize.Net’s strong security measures and detailed subscription management tools make it a reliable choice. It’s particularly suited for mid-to-large SaaS companies prioritizing security and dependable subscription handling.

5. Square

Square

Square offers a payment solution that bridges online and offline transactions, making it a versatile choice for businesses.

Subscription Management Features

Square’s tools for recurring billing are designed to handle SaaS subscriptions effectively. It automates billing processes while ensuring secure card storage and proper customer consent. Here’s a snapshot of its subscription features:

Feature	Description
Recurring Invoicing	Automates billing with flexible scheduling options
Card Storage	Safely stores payment details in a secure vault
Payment Reminders	Sends customizable notifications to customers
Failed Payment Handling	Alerts customers via email if a payment doesn’t go through
Invoice Tracking	Uses consistent invoice IDs for better tracking (e.g., 000001-R-0001)

Square’s pricing structure is another highlight for SaaS businesses.

Pricing Structure

Square’s transparent pricing makes it appealing for businesses of all sizes. Here’s a breakdown of its transaction fees:

Transaction Type	Fee Structure
Online Transactions	2.9% + $0.30
Card on File	3.5% + $0.15
Invoice Payments	3.3% + $0.30
Afterpay Integration	6% + $0.30

Square also offers additional services like email marketing starting at $15/month and advanced access plans at $35/month per location. With no monthly gateway fees and a free basic plan, it’s a cost-effective choice for smaller SaaS businesses.

Integration and Platform Benefits

Square provides APIs and SDKs that make it easy to integrate with SaaS platforms. This ensures smooth functionality for businesses operating both online and offline. Its developer platform supports a unified approach, simplifying operations for SaaS companies.

On top of integration, Square emphasizes security in its payment processes.

Security and Compliance

Square follows strict security measures for recurring payments. Merchants are required to obtain signed credit card authorizations before starting automated billing, helping to reduce disputes and maintain compliance.

Performance and Reliability

Square earned a 4.7/5 rating from Forbes Advisor and was recognized as “Best for startups” by the same source. However, there are a few limitations:

No support for Venmo or Zelle payments
Limited options for complex SaaS customization
Features may not scale well for larger operations

6. 2Checkout (Verifone)

2Checkout

2Checkout, now part of Verifone, offers payment solutions tailored for SaaS businesses, with a focus on managing recurring billing and subscription services. Let’s dive into its features, pricing, and tools that make it a strong choice for subscription-based businesses.

Subscription Management Features

2Checkout provides tools designed to handle recurring revenue efficiently. Here’s a quick look at some of its standout features:

Feature	Description
Revenue Recovery	Recovers up to 20% of failed transactions using Advanced Retry Logic
Card Updates	Updates over 90% of expired cards through its Account Updater Service
Authorization Rates	Improves authorization rates for expired cards by up to 4% with its Internal Account Updater
Billing Automation	Automatically manages prorations, co-terminations, and renewals

These features aim to simplify subscription management while maximizing revenue.

Pricing Structure

2Checkout offers three pricing plans designed to meet different business needs:

Plan	Transaction Fee	Ideal For
2Sell	3.5% + $0.35	Basic digital sales
2Subscribe	4.5% + $0.45	Subscription services
2Monetize	6.0% + $0.60	Complex billing requirements

This tiered pricing ensures businesses can choose a plan that aligns with their specific goals.

Retention Tools

To help businesses reduce churn, 2Checkout includes several retention-focused features:

Options to pause subscriptions
Smart dunning processes with automated retry logic
Expiration reminders to encourage renewals
Discounting tools to promote auto-renewals

These tools are designed to keep customers engaged and subscriptions active.

Integration Capabilities

2Checkout supports integration with over 120 shopping cart platforms, ensuring smooth implementation. Key integration features include:

API access with detailed documentation
Plugins for popular platforms
Instant Notification Service (INS) for real-time updates
Automated order processing for a streamlined checkout experience

These integration options make it easier for businesses to incorporate 2Checkout into their existing systems.

Business Impact

2Checkout has made a strong impact in the SaaS industry. For example, in 2020, U.S. B2C ecommerce, music, and video streaming services processed over $54 billion in payments. The platform also enjoys a solid reputation, with an average user rating of 4.1 out of 5 stars based on 134 reviews.

Advanced Features

Beyond the basics, 2Checkout offers tools that enhance the subscription lifecycle, including:

Support for free and paid trial periods
Smooth plan upgrades
B2B automation to simplify the quote-to-cash process
Detailed revenue analytics for tracking recurring revenue metrics

These advanced capabilities make it a comprehensive solution for subscription-based businesses looking to scale and optimize their operations.

7. GoCardless

GoCardless

GoCardless focuses on direct bank payments and recurring billing, making it a solid fit for SaaS businesses. With over 85,000 companies using its platform, it simplifies subscription management through its ACH debit system.

Key Features for SaaS

GoCardless offers tools that make subscription management easier:

Feature	What It Does
Intelligent Retries	Recovers about 70% of failed payments
International Coverage	Handles payments in over 30 countries
Partner Integrations	Connects with 350+ partner software tools
Lower Payment Costs	Reduces payment expenses by 56% with ACH Pull
Time Savings	Cuts admin tasks by 59%

Pricing Options

GoCardless uses a clear, tiered pricing model for businesses of different sizes:

Plan	Rate	International Transactions	Cap
Standard	0.5% + $0.05	1.5% + $0.05	$5.00
Advanced	0.75% + $0.05	1.75% + $0.05	$6.25
Pro	0.9% + $0.05	1.9% + $0.05	$7.00
Custom	Volume-based pricing for larger businesses

Other fees include $0.50 per refund and $5 per chargeback after 15 monthly instances.

Security Measures

GoCardless prioritizes secure payment processing with:

ISO27001 certification since 2016
Bank-level encryption for data security
PCI DSS compliance for handling customer information
Two-factor authentication for added protection
FCA authorization under Payment Services Regulations 2017

Real-World Savings

Here’s what one client, Capital on Tap, shared about their experience:

“By collecting payments over direct debit and pull ACH versus cards or other payment rails, we’ve probably saved $10, $15 or $20 million.” – Damian Brychy, Chief Operating Officer, Capital on Tap

Premium Features

For businesses looking for more, GoCardless offers advanced tools:

Custom payment pages for $50/month (available on Advanced and Pro plans)
Business name display on customer bank statements for $25/month
Direct Debit guarantee with instant refund protection
Automated billing and invoicing workflows

These features enhance functionality and work seamlessly with its integration network.

Integration Benefits

GoCardless integrates with a wide range of software, simplifying payment collection and accounting. This makes it especially useful for SaaS companies operating across borders or aiming to cut transaction expenses.

Feature Comparison

Take a closer look at the main features of these seven SaaS payment gateways.

Core Features Comparison

Gateway	Monthly Fee	Transaction Fee	Currencies	Key SaaS Features
Stripe	$0	2.9% + $0.30	135+	Smart Retries, Customer Portal, Usage-based Billing
PayPal	$0–$30	2.9% + $0.30	25+	Subscription API, Express Checkout
Braintree	$49	2.59% + $0.49	130+	Recurring Billing, Fraud Protection
Authorize.Net	$25	2.9% + $0.30	12+	Automated Recurring Billing, eCheck
Square	$0	2.6% + $0.10	5+	Invoice Management, Virtual Terminal
2Checkout	$0	3.5% + $0.35	100+	Global Tax Handling, Subscription Analytics
GoCardless	$0	1% + $0.25	30+	Intelligent Retries, Direct Debit

The table covers the basics - fees, currencies, and standout features - but there’s more to each gateway than meets the eye.

Integration and Support Capabilities

Beyond the core features, integration and support options play a huge role in deciding which gateway suits your SaaS business.

Stripe stands out with its developer-friendly tools and detailed API documentation. It supports over 40 local payment methods and includes subscription management features built right in.
Braintree offers custom pricing for specific transaction types. For example, ACH Direct Debit transactions are charged at a lower rate of 0.75%, compared to standard card payments at 2.59% + $0.49.
2Checkout (Verifone) caters to enterprise-level businesses. Although its transaction fees are on the higher side at 3.5% + $0.35, it provides advanced reporting tools, especially useful for international SaaS operations.

Subscription and Global Payment Features

For SaaS companies, managing subscriptions and handling global payments are must-haves. Stripe and GoCardless perform well in reducing involuntary churn and managing multi-currency payments. On the other hand, gateways like PayPal and Braintree offer basic subscription tools but with more limited global reach.

Integration Ecosystem

Each payment gateway integrates with popular business platforms, making setup and ongoing maintenance easier for SaaS companies. Whether you prioritize developer tools, enterprise-level analytics, or global payment capabilities, the right choice depends on your specific needs.

Recommendations

Here’s a breakdown of payment gateway options tailored to different SaaS business needs. These suggestions expand on the feature comparisons discussed earlier.

For Startups and Small SaaS Companies

Stripe is a solid pick for early-stage SaaS businesses. It offers competitive transaction fees without monthly charges, making it a cost-efficient option. Plus, its developer-friendly tools and detailed documentation simplify the integration process.

For Mid-Market SaaS Companies

As your SaaS business grows, Braintree becomes a dependable choice. It provides competitive fees and a suite of tools designed to support scaling businesses.

For Global SaaS Operations

If you’re targeting international markets, 2Checkout (Verifone) stands out. While its fees are higher, it supports transactions in over 150 currencies and accommodates various local payment methods. This makes it a practical solution for handling global payments.

For Enterprise SaaS

Enterprise SaaS companies can benefit from a dual-gateway approach by combining Stripe and GoCardless. Stripe offers a powerful API and excellent subscription management tools, while GoCardless specializes in direct debit processing.

To maximize efficiency, consider integrating with platforms like Chargebee. Many businesses have reported saving over $150,000 annually in operating costs through features like automated revenue recognition. By choosing the right payment gateway setup for your business profile, you can tackle subscription challenges and streamline global payment processing.