6+ Best Shopify Payments Alternatives (2025)

Running an online store on Shopify is one of the fastest ways to start and scale an eCommerce business. With over 4 million active stores, Shopify is a trusted platform for entrepreneurs worldwide.

Shopify Payments — the platform’s built-in payment gateway — simplifies transactions by integrating directly with your store. However, it’s not always the best fit for every merchant. From transaction fees to limited availability in certain countries, many businesses look for the best Shopify Payments alternatives to cut costs, expand internationally, or unlock advanced features.

In this guide, we’ll explore:

What Shopify Payments is and how it works
Why you might consider alternatives
A comparison table of leading options
The best Shopify Payments alternatives, including PayPal, Stripe, Square, Worldpay, and more
Practical FAQs to answer common merchant questions

Let’s dive in.

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What is Shopify Payments?

Shopify Payments Shopify Payments is Shopify’s native payment gateway, powered by Stripe. It allows merchants to accept credit cards, debit cards, and digital wallets without integrating a third-party provider.

✅ Benefits of Shopify Payments:

Seamless integration with your Shopify store
No third-party setup required
Automatic payouts to your bank account
Fraud protection and security included

❌ Limitations of Shopify Payments:

Lack of customization compared to third-party gateways
Limited country availability (not supported in many regions)
Higher fees for currency conversion and cross-border transactions
Restrictions on high-risk industries (e.g., CBD, supplements)

Shopify official guide provides a full breakdown of supported countries and industries.

Why Consider Alternatives to Shopify Payments?

While Shopify Payments is a convenient option for many merchants, there are several reasons why you might consider alternatives:

Transaction Fees: Shopify charges transaction fees if you don’t use Shopify Payments, which can impact profits, especially with high sales volumes.
Limited Payment Options: While Shopify Payments supports major credit cards and some digital wallets, you might need a third-party gateway to offer options like PayPal or cryptocurrency.
High-Risk Businesses: Certain high-risk businesses may find Shopify Payments unavailable, requiring a payment gateway that caters to their industry.
International Expansion: Shopify Payments may not be available in all countries, so a gateway that supports your target markets will be necessary for international expansion.
Customization: Third-party payment gateways may offer more control and specialized features like advanced fraud protection or detailed reporting

Shopify Payments vs Alternatives: Quick Comparison

Here’s a snapshot of popular Shopify Payments alternatives:

Payment Provider	Global Availability	Key Features	Transaction Fees*	Best For
PayPal	200+ countries	Trusted brand, Payflow Pro, QR payments	2.29%–3.49% + $0.49	Global customers, brand trust
Stripe	40+ countries	Customizable API, subscriptions, POS	2.9% + $0.30	Developers, SaaS, recurring billing
Authorize.net	US, Canada, AU, UK	eCheck support, fraud tools	2.9% + $0.30 + $25/mo	SMEs needing reliability
Braintree	45+ countries	PayPal integration, recurring billing	2.59% + $0.49	Scalable businesses
Amazon Pay	Limited (EU, US, JP)	Amazon trust, 1-click checkout	2.9% + $0.30	Amazon-heavy markets
Adyen	150+ countries	Risk management, data analytics	Processing + method fee	Global enterprises
Square	US, UK, CA, JP, AU	POS hardware, invoicing, payroll	2.6% + $0.10	Local + omnichannel retailers
Worldpay	146 countries	Multi-currency, subscription tools	Varies by plan	International merchants

*Fees vary by region and business type.

6+ Shopify Payments Alternatives

PayPal

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Online payments are not limited to a certain number of businesses. PayPal is an identifiable payment platform, pretty much liked by most users globally. It allows merchants in any corner of the world to even receive payments from their customers through a quick process when making purchases. Naturally, PayPal is another accepted alternative to Shopify payments and a few more features besides that create the impression of trust that may lead to increased e-commerce conversion rates.

Key Features:

Would accept payments either via credit or debit card.
It also supports online transactions—invoicing and payments through QR codes.
Gateway payment options: Payflow Pro and Payflow Link.

Transaction Fees:

Typical online checkout transaction costs are 2.29% to 3.49% + $0.49 per transaction.
Credit and debit card transaction costs are 2.99% + $0.49 per transaction.
POS (in-person) fees: 2.29% + $0.09 per transaction.

Stripe

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Stripe is a payment processor known for its customizable payment tools and support for merchants in numerous countries. It provides a flat-rate fee structure without monthly or setup fees, making it a popular choice for businesses seeking flexibility. Stripe’s fees and pricing structure can be an ideal alternative to Shopify payment.

Key Features:

Accepts various payment methods, including credit cards and ACH direct debit.
Offers in-person payments via its POS platform terminal.
Provides tools for subscriptions and improves transaction authorization rates.

Transaction Fees:

Card-not-present payments: 2.9% + $0.30.
Card-present payments: 2.7% + $0.05.
Additional charges may apply for foreign cards, currency conversions, and other features.

Authorize.net

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Authorize.net is a payment gateway service that enables retailers to take credit cards and electronic checks online while providing a secure transaction processing environment. Authorize.net has a long history of providing dependable solutions for organizations of all sizes. Its comprehensive features and security protocols are ideal alternatives to Shopify payment.

Key Features:

Accepts payments from major credit cards and digital payment solutions.
Offers fraud protection tools.
Provides customer information management.

Transaction Fees:

All-In-One Plan: 2.9% + $0.30 each transaction + a $25 monthly cost
Payment Gateway Only Plan: $25 monthly charge plus $0.10 per transaction and a daily batch cost of $0.10.

Braintree

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Braintree, a PayPal service, offers payment processing solutions that accept a variety of payment methods and provide developer-friendly tools. Braintree’s versatile API enables businesses to design personalized payment experiences. Braintree’s custom features and scalability are strong alternatives to Shopify payments.

Key Features:

Accepts PayPal, credit and debit cards, and digital wallets.
Offers fraud protection and data security features.
Provides recurring billing and subscription management tools.

Transaction Fees:

2.59% + $0.49 per transaction.
Additional fees may apply based on the payment method and specific features used.

Amazon Pay

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Amazon Pay enables customers to use the payment information stored in their Amazon accounts to make purchases on third-party websites. This service streamlines the checkout process for millions of Amazon users. Amazon Pay’s convenience and trust factor can boost conversion rates, making it a viable alternative to Shopify payments.

Key Features:

Provides a familiar and trusted payment experience for Amazon customers.
Offers fraud protection and A-to-z Guarantee.
Supports mobile payments and voice commerce.

Transaction Fees:

Vary based on transaction type and region.
Typically, the transaction fee is roughly 2.9% + $0.30.
Cross-border transactions may attract additional costs.

Adyen

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Adyen is a payment platform that enables businesses to take payments from anywhere in the globe. It offers sophisticated data analytics and reporting across numerous platforms, including online, mobile, and in-store. Adyen’s unified platform and worldwide reach position it as a viable candidate for firms looking for alternatives to Shopify Payments.

Key Features:

Supports various payment methods globally.
Offers risk management and fraud prevention tools.
Provides detailed data analytics and reporting.

Transaction Fees:

Adyen charges a processing fee + a payment method fee.
Processing fees are typically around $0.12 per transaction.
Payment method fees vary depending on the payment method and region.

Final Thoughts

Choosing the right Shopify payment alternative is a critical decision for any online business. Consider your specific needs, such as transaction fees, features, target audience, and technical requirements. If you’re having trouble with manual payment methods not showing on Shopify checkout, or you’re exploring options like TikTokShop payments with Shopify, carefully research each option to ensure it meets your criteria.

AQs About Shopify Payments Alternatives

1. Is Shopify Payments free?

No. While there are no setup fees, Shopify Payments charges transaction fees (2.9% + $0.30 in the US).

2. Can I use PayPal and Shopify Payments together?

Yes. You can enable both, allowing customers to choose their preferred method at checkout.

3. What is the cheapest Shopify payment gateway?

It depends on your region and volume. Stripe and Square often offer competitive flat rates, while Adyen and Worldpay give better deals for enterprise merchants.