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Best Payment Gateway for Small Businesses (2025 Guide) — Fees, Features & Comparison

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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

SEO Keywords:
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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

SEO Keywords:
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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

SEO Keywords:
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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)

SEO Keywords:
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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

SEO Keywords:
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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

SEO Keywords:
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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)

  1. Create a business account
  2. Complete KYC/KYB
  3. Add your bank account
  4. Integrate the gateway into your website
  5. Enable digital wallets (Apple/Google Pay)
  6. Test payments
  7. 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:

🥇 Stripe (best overall)

🥈 Square (best for retail)

🥉 Shopify Payments (best for ecommerce)

FinTechAdmin
FintechAdmin: Technology Savvy | Banking | FinTech | Payments