Best Shopify Third Party Payment Providers: How to Choose the Right Option for Your Store

Choosing the best Shopify third party payment providers is not just about finding the most famous payment brand. For a Shopify merchant, the right payment provider affects checkout conversion, customer trust, payment method coverage, transaction fees, payout timing, fraud risk, refunds, reconciliation, and international expansion.

Some Shopify stores can rely on Shopify Payments as the default option. Others need Shopify third party payment providers because they sell in markets where Shopify Payments is unavailable, need local payment methods, already have a processor relationship, operate in a specialized industry, or want more payment flexibility.

Shopify's official help page states that merchants can choose from over 100 credit card payment providers for their Shopify store. Shopify also explains that third-party providers can be used as the sole credit card processor or alongside Shopify Payments to access additional payment methods such as Shop Pay and local payment methods.

Key Takeaways

• The best Shopify third party payment providers depend on country, customer payment preferences, business model, fees, checkout experience, and operational needs.
• Shopify supports direct providers and external providers. Direct providers let customers complete checkout inside the Shopify store, while external providers redirect customers to a third-party checkout page.
• Shopify says third-party transaction fees apply to third-party and alternate payment gateways, even when Shopify Payments is activated, with some exclusions such as PayPal and manual payments when Shopify Payments is active.
• Shopify's own payment gateway comparison lists Shopify Payments, Stripe, PayPal, Adyen, Authorize.net, Square Payments, and Clover as major payment gateway options, but the best provider still depends on the merchant's needs.
• For stores targeting international customers, local payment methods can matter as much as card acceptance.
• The phrase "best third party payment providers for Shopify" should be answered with a decision framework, not a one-size-fits-all ranking.
• Antom is relevant for merchants that need global and local payment acceptance, payment orchestration, risk management, and cross-border payment coverage beyond a basic Shopify payment setup.

What Are Shopify Third Party Payment Providers?

Shopify third party payment providers are external payment companies that Shopify merchants can use to accept customer payments instead of, or in some cases alongside, Shopify Payments.
They may support:

• credit cards;
• debit cards;
• digital wallets;
• local payment methods;
• bank transfers;
• BNPL;
• recurring payments;
• multi-currency payments;
• hosted checkout;
• payment gateway services;
• fraud tools;
• refunds and disputes;
• settlement reporting.

Shopify supports two types of credit card payment providers: direct providers and external providers. With a direct provider, customers complete their purchase directly inside the Shopify store. With an external provider, customers are redirected to a checkout page hosted outside the online store.
This distinction matters because the checkout experience can affect customer trust and conversion.

Shopify Payments vs Third Party Payment Providers

Why Use a Third Party Payment Provider on Shopify?

1. Shopify Payments Is Not Available in the Merchant's Country

2. Customers Prefer Local Payment Methods

3. The Store Already Has a Processor Relationship

4. The Business Needs Specialized Features

5. The Store Sells Internationally

6. The Merchant Wants Backup Payment Options

The Cost Issue: Third Party Transaction Fees

• the third-party provider's processing fee;
• Shopify's third-party transaction fee;
• refund fees;
• chargeback fees;
• FX fees;
• payout fees;
• monthly fees;
• app or integration fees;
• operational cost for reporting and reconciliation.

A provider that looks cheaper at the processor level may become more expensive once Shopify's additional fees and operational costs are included.

Best Third Party Payment Providers for Shopify by Use Case

Shopify Payments

• Shopify Payments is available in the merchant's country;
• the store wants simple setup;
• the merchant wants centralized payment reporting;
• the store wants to avoid extra third-party transaction fees;
• the business uses Shopify POS;
• the store does not need highly specialized local methods.

Shopify states that Shopify Payments supports online and in-person payment processing through a single platform, and that merchants can track orders and payments in one place.
However, Shopify Payments may not be enough if the merchant needs local methods that are not supported in a target market, custom payment flows, or specific PSP relationships.

PayPal

• the store wants a familiar wallet option;
• customers expect PayPal in the target market;
• the merchant sells internationally;
• the store wants an alternative to card-only checkout;
• the business wants to support customers who prefer not to enter card details directly.

However, PayPal should be evaluated by cost, dispute handling, account review risk, and reporting needs.

Stripe

• the business runs subscription products;
• the merchant needs custom payment logic;
• the store has developer resources;
• the business operates across multiple channels;
• the company wants API flexibility.

For Shopify merchants, the key question is whether Stripe is available and appropriate in the merchant's Shopify region and whether third-party transaction fees make sense.

Adyen

• the merchant sells in multiple countries;
• the business has higher payment volume;
• the company needs local acquiring or local method coverage;
• the merchant wants enterprise reporting;
• the store has more complex payment operations.

For smaller Shopify stores, Adyen may be more advanced than needed. For global or enterprise merchants, it may be a serious candidate.

Authorize.net

• the merchant already has a merchant account;
• the business wants a gateway layer;
• the store needs card acceptance with a more traditional setup;
• the merchant values fraud and security tools;
• the business wants to keep a processor or acquirer relationship.

Shopify's gateway article lists Authorize.net for advanced security.

Square and Clover

• the business sells in person;
• POS hardware matters;
• the store operates pop-ups or events;
• the business needs simple card-present payments;
• the merchant wants retail or restaurant-friendly workflows.

For Shopify merchants, the key issue is whether the provider fits the online store, POS workflow, and reporting requirements.

Local PSPs and Regional Payment Providers

• iDEAL in the Netherlands;
• Bancontact in Belgium;
• Sofort or SEPA-related methods in Europe;
• Pix in Brazil;
• OXXO-style cash payments in Mexico;
• local wallets in Southeast Asia;
• QR payments in parts of APAC;
• bank transfer methods in Europe and Asia;
• mobile money in selected African markets.

Third-party PSPs can be valuable when they support localized payment methods that Shopify Payments or card-only checkout does not fully cover.

Direct Provider vs External Provider

Best Shopify Third Party Payment Providers: Evaluation Checklist

Best Third Party Payment Providers for Shopify: Shortlist by Merchant Type

Payment Methods Matter More Than Provider Names

When Shopify Payments Is Enough

• it is available in the merchant's country;
• most customers use supported cards or wallets;
• the store wants simple setup;
• the merchant wants centralized reporting;
• additional third-party transaction fees would reduce margin;
• the business does not need niche local payment methods;
• the store does not need advanced enterprise PSP features.

For many standard Shopify merchants, this is the most practical setup.

When a Third Party Provider Is Better

• Shopify Payments is not available;
• the target market needs specific local payment methods;
• the store already has a processor relationship;
• the merchant needs advanced fraud tools;
• the business needs multi-currency settlement;
• the store sells high-ticket or specialized products;
• enterprise reporting is required;
• the merchant wants backup payment coverage;
• a specific market requires a local PSP.

The key is to calculate the total value, not just the added cost.

How to Compare Total Cost

How Antom Fits Shopify and Cross-Border Payment Strategy

• global and local payment method acceptance;
• cards and local cards;
• digital wallets and online banking;
• one-time payments;
• subscription and recurring payment scenarios;
• payment orchestration;
• smart routing and custom routing;
• payment risk management;
• transaction operations;
• reconciliation and billing support;
• multi-currency payment acceptance;
• cross-border expansion across APAC, LATAM, Europe, the Middle East, and other regions.

A Shopify merchant should still verify provider availability, integration route, technical requirements, and regional compatibility before implementation. But for merchants expanding internationally, the broader issue is clear: payment success depends on local method coverage, payment routing, settlement visibility, and risk management, not only on whether a provider appears in a generic Shopify gateway list.

Practical Example: Shopify Store Expanding Internationally

• European customers ask for local bank methods;
• Southeast Asian customers prefer wallets and QR payments;
• LATAM customers need local cards, Pix, or cash-based methods;
• card authorization rates vary by country;
• FX and settlement reporting become more complex;
• customer support receives more failed payment questions;
• finance wants payment reports by market and method.

At this stage, the store should not only search for the “best Shopify third party payment providers.” It should map customer payment behavior by market and then evaluate whether Shopify Payments, PayPal, a regional PSP, a global PSP, or a payment orchestration setup best supports that growth plan.

Common Mistakes When Choosing Shopify Third Party Payment Providers

Mistake 1: Choosing From a Generic List

A generic provider list does not account for your country, target markets, products, margins, customer behavior, or Shopify plan.

Mistake 2: Ignoring Shopify Third-Party Transaction Fees

A provider's own fees are not the full cost. Shopify may charge extra transaction fees for third-party and alternate payment gateways.

Mistake 3: Choosing Only by Brand Recognition

A famous provider may not support the local payment methods your customers prefer.

Mistake 4: Ignoring Direct vs External Checkout

External checkout can be useful, but redirecting customers away from the store may add friction.

Mistake 5: Not Testing Refunds and Disputes

Before choosing a provider, merchants should test refunds, partial refunds, chargebacks, and payment status updates.

Mistake 6: Forgetting Reconciliation

Finance teams need clean reports showing orders, payments, fees, refunds, chargebacks, and settlements.

Mistake 7: Not Planning for Global Expansion

A payment setup that works for a domestic Shopify store may not support international checkout expectations.

Summary

The best Shopify third party payment providers are not the same for every store. Shopify Payments is often the easiest starting point when it is available and when customer payment needs are straightforward. PayPal can add customer trust. Stripe-style providers can support subscriptions and custom payment logic. Adyen-style providers can support enterprise and international selling. Authorize. net-style gateways can support more traditional payment setups. Local PSPs can support market-specific methods that customers prefer.

The right choice depends on country availability, Shopify plan, third-party transaction fees, checkout type, customer location, local payment methods, payout timing, refunds, chargebacks, fraud tools, reporting, support, and scalability.

For merchants expanding internationally, the decision should move beyond “which provider is popular?” toward “which payment setup helps customers pay in the way they trust most?”

Antom helps businesses accept local and global payments across 200+ payment markets through one integration, with support for payment orchestration, smart routing, risk management, transaction operations, and reconciliation.

Explore Antom's payment service provider capabilities to see how your Shopify or cross-border commerce business can support customers with scalable global and local payment options.