Choosing the right payment gateway is one of the most important decisions for any small business. Whether you run an online store, a consulting service, or a local business with both online and offline payments—your payment processor impacts fees, conversion rates, payouts, and customer trust.
In this 2025 guide, we compare the best payment gateways for small businesses, including Stripe, PayPal, Square, Shopify Payments, Wise Business, Payoneer, Helcim, and more.
We also break down fees, features, payout times, and which platform is best for your type of business.
⭐ Quick Summary: Best Payment Gateways for Small Businesses (2025)
| Payment Gateway | Best For | Key Features | Avg Fees (US) |
|---|---|---|---|
| Stripe | Online stores, SaaS, global payments | Advanced APIs, subscriptions, global currency support | 2.9% + 30¢ |
| PayPal | Freelancers, digital goods, quick checkout | Instant brand trust, fast onboarding | 3.49% + 49¢ |
| Square | Retail stores, restaurants | POS + online payments + invoicing | 2.6% + 10¢ |
| Shopify Payments | Ecommerce stores | Low fees, integrated checkout | 2.4–2.9% |
| Helcim | Transparent pricing | Interchange+ pricing, low fees | Varies |
| Wise Business | International payouts | Lowest FX fees, multi-currency accounts | 0.4–1.0% FX |
| Payoneer | Global freelancers, marketplaces | Fast global payouts | 1–3% |
| Authorize.Net | Traditional merchants | Advanced fraud protection | From 2.9% + 30¢ |
🔍 What Is a Payment Gateway?
A payment gateway processes online transactions by connecting your website or app to the bank. It handles:
- Card authorization
- Encryption
- Fraud checks
- Settlement
- Payouts
The right gateway reduces fees, improves conversion, and supports global customers.
Let’s break down each gateway with pros, cons, fees, and who it’s best suited for.
1. Stripe — Best Overall Payment Gateway for Small Businesses
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Stripe is the most advanced and most widely used payment gateway globally. It supports over 135 currencies, subscription billing, digital wallets, and advanced fraud protection.
Pros
- Supports SaaS, ecommerce, subscriptions, marketplaces
- Global payments with low FX markup
- Excellent APIs
- Supports Apple Pay & Google Pay
- Extremely reliable
Cons
- Slightly technical setup
- Not ideal for complete beginners
Fees
- 2.9% + 30¢ per transaction (US)
- Additional 1% for international cards
Best For
- Online stores
- SaaS subscriptions
- Digital goods businesses
- Global scaling businesses
2. PayPal — Best for Fast Checkout & Freelancers
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PayPal is trusted worldwide and is great for beginners due to instant onboarding.
Pros
- Instant customer trust
- Built-in buyer protection
- Easy integration
- Perfect for one-time payments
Cons
- Higher fees
- Funds can sometimes be held
Fees
- 3.49% + 49¢ (US)
- Cross-border fee applies
Best For
- Freelancers
- Digital products
- Beginners
3. Square — Best for Local Retail & Restaurants
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Square combines POS terminals + online payments, making it perfect for hybrid businesses.
Pros
- Free POS
- Invoicing + appointments
- Excellent for physical stores
Cons
- Limited in some countries
Fees
- 2.6% + 10¢ (in-person)
- 2.9% + 30¢ (online)
Best For
- Retail
- Food businesses
- Local services
4. Shopify Payments — Best for Ecommerce Stores
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If your store is on Shopify, this is the best option.
Pros
- No transaction fees
- High-converting checkout
- Integrated fraud system
Cons
- Only works with Shopify
Fees
- 2.4–2.9%
Best For
- Ecommerce brands
- Dropshipping
- Print-on-demand
5. Wise Business — Best for International Payments (Lowest FX Fees)
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Wise is perfect for freelancers and businesses that receive payments globally.
Pros
- Lowest FX fees
- Multi-currency receiving accounts
- Transparent pricing
Cons
- Not a traditional gateway for checkout
- Limited integrations
Fees
- FX: 0.4%–1%
Best For
Global freelancers
Agencies
Remote teams
6. Payoneer — Best for Global Freelancers & Marketplaces
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Payoneer offers fast payouts from marketplaces like Upwork, Fiverr, Amazon, Walmart, etc.
Pros
- Great for international payouts
- Fast transfers
- Multi-currency accounts
Cons
- Not ideal for ecommerce checkout
Fees
-
1%–3% depending on sender
Best For
- Freelancers
- Marketplace sellers
7. Helcim — Best for Low Transparent Fees
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Helcim uses interchange-plus pricing—often the cheapest for growing businesses.
Pros
- Transparent fees
- Volume-based discounts
Cons
-
Not available in all countries
Best For
- Medium-sized businesses
- Subscription businesses
📉 Fee Comparison (2025)
| Gateway | Standard Fee | International Fee | Payout Time |
|---|---|---|---|
| Stripe | 2.9% + 30¢ | +1% | 2 days |
| PayPal | 3.49% + 49¢ | High | Instant–3 days |
| Square | 2.6% + 10¢ | N/A | 1–2 days |
| Shopify Payments | 2.4–2.9% | +1% | 2 days |
| Wise | 0.4–1% FX | Low | Instant–2 days |
| Payoneer | 1–3% | Low | 1–2 days |
🧠 How to Choose the Right Payment Gateway (Decision Guide)
Choose Stripe if:
- You want global customers
- You run subscriptions
- You have a digital or SaaS product
Choose PayPal if:
- You’re a freelancer
- You want instant checkout
- You’re starting with no technical experience
Choose Square if:
-
You run a retail store, salon, café, or restaurant
Choose Shopify Payments if:
-
Your store is built on Shopify
Choose Wise/Payoneer if:
-
You receive international payments frequently
🛠️ How to Set Up a Payment Gateway (Simple Steps)
- Create a business account
- Complete KYC/KYB
- Add your bank account
- Integrate the gateway into your website
- Enable digital wallets (Apple/Google Pay)
- Test payments
- Go live
❓ FAQ
- Which payment gateway has the lowest fees?
Wise (for FX), Helcim (for domestic), and Stripe (for global cards).
- Which gateway is best for US small businesses?
Stripe or Square.
- Which supports both online and offline payments?
Square.
- Which gateway is best for global ecommerce?
Stripe + Wise combo.
✅ Final Recommendation
If you want the best all-around payment gateway for 2025, choose: