Yes, Shopify charges additional fees when you choose a payment processor other than Shopify Payments. But don’t run off just yet! There are major benefits to using an alternative payment processor.

Their fee structure affects thousands of merchants who want to use their preferred payment gateway while staying on Shopify’s platform. You’re not alone and you need answers.

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What Are Third-Party Transaction Fees?

Shopify applies third-party transaction fees whenever you process payments through external providers like PayPal, Adyen, Authorize.net, or other payment gateways. These fees come on top of what your chosen payment processor already charges you.

The fee structure breaks down by plan level:

• Basic Shopify: 2% per transaction
• Shopify Plan: 1% per transaction
• Advanced Shopify: 0.6% per transaction
• Shopify Plus: 0.2% per transaction

Shopify covers the cost of providing a secure checkout platform and integrating with external payment providers through these fees. The company positions this as necessary infrastructure to support third-party integrations.

However, we know that the platform makes their money primarily with Shopify Payments. If you decide not to use their payment service, they still want a cut.

Recent Changes to the Fee Structure

Shopify expanded its third-party fee policy in May 2025. Stores created on or after May 12, 2025, now face third-party transaction fees when customers use store credit or gift cards as payment methods. This change affects even stores using Shopify Payments as their primary gateway.

For example, if a customer pays $50 with a credit card and $10 with store credit, Shopify charges the third-party fee only on the $10 store credit portion.

The Real Cost Impact

Let’s examine what these fees mean for your business. A store processing $20,000 monthly through a third-party processor on the Basic plan pays an additional $400 in Shopify fees alone.

This amount comes before considering your payment processor’s own fees.

For a business handling $50,000 monthly, the additional cost reaches $1,000 per month on the Basic plan. These numbers add up to $12,000 annually in extra fees just for using your preferred payment processor.

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Why Businesses Choose Third-Party Processors Despite the Fees

Many merchants accept Shopify’s additional fees because third-party processors offer compelling advantages.

Global Reach and Currency Support

Third-party processors often support more countries and currencies than Shopify Payments. International businesses frequently need this broader coverage to serve their customer base effectively.

Advanced Features and Analytics

Other payment processors provide more sophisticated fraud protection, subscription billing capabilities, and detailed analytics. These features can justify the additional cost for merchants with complex needs.

Customer Trust and Familiarity

Established payment brands build customer confidence during checkout. Many shoppers feel more comfortable entering payment information with recognizable names like PayPal, which can improve conversion rates.

Industry-Specific Requirements

Some businesses operate in industries where Shopify Payments isn’t available or doesn’t meet regulatory requirements. These merchants have no choice but to use alternative processors.

Existing Relationships and Better Rates

Established businesses often negotiate better processing rates with their existing payment partners. Even with Shopify’s additional fee, the total cost might still be lower than Shopify Payments for high-volume merchants.

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Strategies to Minimize Third-Party Fees

Smart merchants use several approaches to reduce the impact of third-party transaction fees.

Plan Optimization

Upgrading to a higher Shopify plan reduces the third-party fee percentage. The Advanced plan’s 0.6% fee versus the Basic plan’s 2% fee can save significant money for growing businesses.

You should only upgrade your plan if it makes sense for your business, as more advanced plans cost more per month.

Hybrid Payment Approach

Some merchants offer both Shopify Payments and third-party options, allowing customers to choose while encouraging the fee-free option through incentives or positioning.

Volume Analysis

Calculate your total payment processing costs including both processor fees and Shopify’s additional charges. Sometimes the math favors staying with third-party processors despite the extra cost.

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Making the Right Choice for Your Business

The decision between Shopify Payments and third-party processors depends on your specific situation. Consider the following factors.

• Geographic Requirements: If you serve customers in regions where Shopify Payments isn’t available, third-party processors become necessary.
• Feature Needs: Businesses requiring advanced fraud protection, recurring billing, or detailed analytics might find third-party processors worth the extra cost.
• Customer Preferences: If your customers strongly prefer specific payment methods, accommodating them might improve sales enough to offset the additional fees.
• Total Cost Analysis: Calculate all fees including processing rates, monthly charges, and Shopify’s additional fees to determine your most cost-effective option.

The Bottom Line

Shopify’s third-party transaction fees create an additional cost layer for merchants who choose alternative payment processors. While these fees can add up quickly, many businesses find that third-party processors still provide better value through superior features, broader geographic support, or customer trust benefits.

Understand your total cost of payment processing and weigh it against the benefits each option provides. For some merchants, paying Shopify’s additional fees makes perfect business sense when it enables better customer service, international expansion, or access to specialized features.

Before making your decision, calculate the real numbers for your business volume and consider both the immediate costs and long-term benefits of each payment processing approach.

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