Shopify Payments vs third-party PSPs: “Hidden” costs and fees you need to know

Imagine this: you’ve spent months perfecting your Shopify store, optimizing product pages, crafting compelling marketing campaigns, and fine-tuning your checkout process. But what if an invisible fee was quietly eating into your profits?

Choosing the right payment processor is one of the most critical decisions for any Shopify merchant. While platforms like Mollie, Multisafepay, and Pay.nl offer flexibility and advanced features, they come with a catch: Shopify charges additional transaction fees when you opt out of its native solution, Shopify Payments. These hidden costs can add up quickly, impacting your bottom line and long-term profitability.

In this guide, we’ll dive deep into the differences between Shopify Payments and third-party Payment Service Providers (PSPs), uncover the hidden fees you need to know, and equip you with actionable insights to make the best decision for your business. 

What is Shopify Payments?

Shopify Payments is Shopify’s native payment gateway, designed to simplify the checkout process for merchants and customers alike. As an integrated solution, it eliminates the need for third-party payment processors, offering a seamless experience that aligns perfectly with the Shopify ecosystem.

How does Shopify Payments work?

At its core, Shopify Payments acts as both a payment processor and a merchant account rolled into one. When a customer initiates a purchase, Shopify Payments securely processes the transaction through its partnership with leading financial institutions like Adyen (in Europe) and Stripe (in regions like the USA, Canada, and Australia). This ensures smooth and reliable transactions across different currencies and regions.

Here’s a breakdown of how Shopify Payments works:

1. Customer initiates payment: The customer selects their preferred payment method, such as credit cards, debit cards, or digital wallets like Apple Pay.
2. Transaction processing: Shopify Payments securely transmits the payment information through its encrypted payment gateway.
3. Authorization and authentication: The system verifies the transaction details, checks for sufficient funds, and seeks approval from the issuing bank.
4. Completion of payment: If approved, the funds are transferred directly to your Shopify account, bypassing the need for a separate merchant account or external processor. For more details on how payments are processed, visit Shopify’s official guide on payment gateways.

Key benefits of Shopify Payments

• No additional fees: Unlike third-party PSPs, Shopify Payments does not incur extra transaction fees from Shopify. This makes it a cost-effective choice for merchants looking to maximize profitability.
• Unified dashboard: With Shopify Payments, all your orders, payments, and financial data are centralized in one place. This simplifies tracking and reporting, giving you a complete view of your business’s performance. Learn more about managing your finances with Shopify Payments here.
• Instant payouts: Funds are deposited directly into your bank account, often within days, ensuring better cash flow management.
• Support for local currencies and payment methods: Whether you’re selling in euros, dollars, or pounds, Shopify Payments supports multiple currencies and popular local payment methods, enhancing the checkout experience for international customers.
• PCI compliance: Shopify Payments is fully PCI DSS compliant, meaning your customers’ sensitive financial data is protected at all times. For more information on security standards, refer to Shopify’s PCI compliance guide.

Why choose Shopify Payments over third-party PSPs?

While third-party PSPs like Mollie, Multisafepay, and Pay.nl offer advanced features and flexibility, they come with a significant drawback: Shopify charges additional transaction fees when you opt out of Shopify Payments. These fees can range from 0.6% to 2%, depending on your Shopify plan. For businesses processing thousands of dollars in transactions monthly, these costs can quickly add up.

By choosing Shopify Payments, you not only avoid these hidden fees but also benefit from a streamlined integration that’s purpose-built for Shopify stores. This means fewer technical headaches, faster setup times, and a more cohesive shopping experience for your customers. To explore Shopify Payments further, visit their official page.

What are third-party PSPs?

While Shopify Payments offers a seamless and integrated solution, many merchants opt for third-party Payment Service Providers (PSPs) like Mollie, Multisafepay, and Pay.nl. These platforms provide flexibility and advanced features that cater to specific business needs. However, they also come with trade-offs, most notably, the additional transaction fees imposed by Shopify when used instead of its native payment processor.

What is a third-party PSP?

A third-party PSP is an external payment processor that integrates with Shopify to facilitate transactions. Unlike Shopify Payments, which is built directly into the platform, third-party PSPs operate independently and often require additional setup. Examples include:

• Mollie: Known for its localized payment methods and user-friendly interface.
• Multisafepay: Offers advanced fraud prevention tools and multi-currency support.
• Pay.nl: Specializes in customizable checkout experiences and localized payment solutions.

These providers are designed to handle a wide range of payment methods, from credit cards and digital wallets to bank transfers and buy-now-pay-later options. They’re particularly popular among businesses operating in regions where local payment preferences differ significantly from global standards.

Key features of third-party PSPs

Third-party PSPs offer several advantages that make them appealing to certain merchants:

1. Flexibility in payment methods:
   Third-party PSPs often support a broader range of payment methods, including local options like iDEAL (Netherlands), Bancontact (Belgium), and Sofort (Germany). This can enhance the checkout experience for international customers who prefer using familiar payment systems.
2. Advanced features:
   Many third-party PSPs provide tools like:
   • Fraud prevention: Advanced algorithms to detect and prevent fraudulent transactions.
   • Currency conversion: Real-time currency conversion for cross-border sales.
   • Customizable checkouts: Options to tailor the checkout process to match your brand’s identity.
3. Scalability:
   Third-party PSPs are often designed to handle large transaction volumes, making them suitable for growing businesses or enterprises with complex payment needs.

The catch: Additional transaction fees

While third-party PSPs offer flexibility and advanced features, they come with a significant drawback: Shopify charges additional transaction fees when you use them instead of Shopify Payments. These fees vary depending on your Shopify plan but typically range from 0.6% to 2% of each transaction. For example:

• On the Basic Shopify Plan, the fee is 2%
• On the Shopify Plan, the fee is 1%
• On the Advanced Shopify Plan, the fee is 0.6%

This means that if your store processes €50,000 in monthly revenue using a third-party PSP, you could incur an additional €500–€1,000 in fees annually, a cost that can quickly add up for growing businesses.

Let’s break down a real-world scenario to illustrate the financial impact of these hidden costs:

Why does Shopify charge these fees?

Shopify incentivizes merchants to use Shopify Payments as their primary payment processor. By doing so, Shopify ensures a streamlined ecosystem where all financial data is centralized within the platform. When merchants opt for third-party PSPs, Shopify loses some control over the payment process and introduces potential complexities, such as reconciliation and reporting. To offset these challenges, Shopify imposes additional transaction fees.

Hidden costs that merchants often overlook

Many merchants are unaware of these additional fees until after they’ve integrated a third-party PSP. This lack of transparency can lead to unexpected costs that impact profitability. For instance:

• A merchant using Mollie might assume they’re only paying Mollie’s transaction fees, not realizing that Shopify also charges an extra 1% on top of those fees.
• Similarly, businesses using Multisafepay or Pay.nl may overlook the cumulative effect of these fees over time.

To avoid surprises, it’s crucial to carefully evaluate the total cost of using a third-party PSP versus Shopify Payments. For more information on Shopify’s fee structure, refer to their official guide on transaction fees.

When should you consider a third-party PSP?

Despite the additional fees, there are scenarios where third-party PSPs might be the better choice:

1. Localized payment needs: If your target market prefers specific payment methods not supported by Shopify Payments, a third-party PSP might be necessary.
2. Advanced features: Businesses requiring specialized tools like multi-currency support or advanced fraud prevention may benefit from third-party PSPs.
3. Existing partnerships: Some merchants already have established relationships with PSPs like Mollie or Multisafepay, making the transition to Shopify smoother.

However, always weigh these benefits against the hidden costs to ensure you’re making the most cost-effective decision for your business.

Shopify Payments vs. third-party PSPs: A detailed comparison

Choosing between Shopify Payments and a third-party Payment Service Provider (PSP) is one of the most critical decisions for any Shopify merchant. Both options have their strengths and weaknesses, and understanding the differences will help you make an informed decision that aligns with your business goals. Below, we’ll compare these two payment solutions across several key factors to help you evaluate which one is the best fit for your store.

1. Integration complexity

• Shopify Payments:
  Shopify Payments is fully integrated into the Shopify platform, meaning there’s no need for additional setup or technical configuration. It works out of the box, offering a seamless experience for both merchants and customers.
  • Pros: No setup headaches, automatic updates, and centralized reporting.
  • Cons: Limited flexibility if your business requires specialized features not offered by Shopify Payments.
• Third-party PSPs (e.g., Mollie, Multisafepay, Pay.nl):
  Third-party PSPs require additional integration steps, such as installing apps, configuring APIs, or setting up custom workflows. While this allows for more customization, it can also introduce complexity and potential compatibility issues.
  • Pros: Greater flexibility for businesses with unique needs.
  • Cons: Requires technical expertise and ongoing maintenance.

2. Transaction fees

• Shopify Payments:
  One of the biggest advantages of Shopify Payments is that it eliminates additional transaction fees imposed by Shopify. You only pay the standard credit card processing fees, which vary depending on your Shopify plan:
  • Basic Shopify: 2.9% + €0.30 per transaction
  • Shopify: 2.6% + €0.30 per transaction
  • Advanced Shopify: 2.4% + €0.30 per transaction
• Third-party PSPs:
  When using a third-party PSP, Shopify charges an additional transaction fee on top of the PSP’s own fees. These fees are:
  • Basic Shopify: 2%
  • Shopify: 1%
  • Advanced Shopify: 0.6%

For example, if you’re using Mollie on the Shopify Plan, you’ll pay Mollie’s transaction fees plus an additional 1% to Shopify. This can add up significantly over time, especially for high-volume stores.

3. Supported regions and payment methods

• Shopify Payments:
  Shopify Payments supports multiple regions and currencies, leveraging partnerships with Adyen (Europe) and Stripe (USA, Canada, Australia). However, it may not always support every local payment method preferred in specific markets.
  • Pros: Broad international reach, seamless multi-currency support.
  • Cons: Limited availability of niche or regional payment methods.
• Third-party PSPs:
  Platforms like Mollie, Multisafepay, and Pay.nl excel in supporting localized payment methods, such as iDEAL (Netherlands), Bancontact (Belgium), and Sofort (Germany). This makes them ideal for businesses targeting specific regions.
  • Pros: Wide range of local payment options.
  • Cons: Additional fees from Shopify for using third-party providers.

4. Unique features

• Shopify Payments:
  Shopify Payments offers core features like instant payouts, unified reporting, and PCI compliance built directly into the platform. It’s designed to simplify operations and provide a cohesive experience for merchants.
  • Pros: Easy-to-use dashboard, centralized data, and robust security.
  • Cons: Limited advanced features like fraud prevention tools or customizable checkouts.
• Third-party PSPs:
  Third-party PSPs often provide advanced features.
  • Pros: Specialized tools for complex needs.
    • Fraud prevention: Tools to detect and prevent fraudulent transactions.
    • Currency conversion: Real-time exchange rates for cross-border sales.
    • Customizable checkouts: Options to tailor the checkout process to match your brand.
  • Cons: Higher costs due to Shopify’s additional transaction fees.

5. Security compliance

Both Shopify Payments and third-party PSPs comply with industry standards like PCI DSS (Payment Card Industry Data Security Standard). However, Shopify Payments simplifies compliance by handling all security requirements internally, while third-party PSPs may require additional steps to ensure full compliance.

6. Settlement time frames

• Shopify Payments:
  Funds are typically deposited into your bank account within 2–3 business days, ensuring smooth cash flow management.
  • Pros: Faster access to funds compared to some third-party PSPs.
• Third-party PSPs:
  Settlement times vary depending on the provider. Some PSPs may take longer to process payouts, which can impact your cash flow.
  • Pros: Certain PSPs offer faster payouts for an additional fee.
  • Cons: Longer settlement times for standard plans.

7. Customer support

• Shopify Payments:
  Shopify provides 24/7 customer support for all merchants using Shopify Payments. This ensures quick resolution of any issues related to payments or integrations.
  • Pros: Reliable support is included with your Shopify subscription.
• Third-party PSPs:
  Support quality varies by provider. While platforms like Mollie and Multisafepay offer responsive support, others may have limited availability or slower response times.
  • Pros: Dedicated support for specific PSP-related issues.
  • Cons: Inconsistent support experiences across providers.

8. Scalability and flexibility

• Shopify Payments:
  Shopify Payments scales seamlessly as your business grows. Whether you’re processing €10,000 or €1 million in revenue, the system remains reliable and efficient.
  • Pros: Built to handle growth without significant fee increases.
• Third-party PSPs:
  Third-party PSPs are often designed for large-scale operations, making them suitable for enterprises with complex payment needs. However, the additional fees from Shopify can become prohibitive as transaction volumes increase.
  • Pros: Advanced scalability for high-volume businesses.
  • Cons: Higher costs at scale due to Shopify’s additional fees.

Comparison table: Shopify Payments vs. third-party PSPs

Factors to consider when choosing a payment processor

Choosing the right payment processor is crucial for your business’s success. Here are nine key factors to help you decide between Shopify Payments and third-party PSPs like Mollie, Multisafepay, or Pay.nl:

1. Supported payment options

Understand your customers’ preferences. Older generations prefer credit/debit cards, while younger shoppers favor digital wallets (e.g., Apple Pay) or buy-now-pay-later options. If your audience prefers localized methods (e.g., iDEAL in the Netherlands), third-party PSPs may be necessary.

2. Fee structures

Cost matters. Compare fees carefully:

• Shopify Payments: No additional transaction fees from Shopify. Standard credit card processing fees apply.
• Third-party PSPs: Shopify charges an extra 0.6%–2%, on top of the PSP’s own fees.

Calculate total costs to avoid surprises.

3. Security compliance

Both Shopify Payments and third-party PSPs comply with PCI DSS standards. However:

• Shopify Payments: Simplifies compliance by handling security internally.
• Third-party PSPs: May require additional steps for full compliance.

Look for features like encryption and fraud detection.

4. Compatibility

Ensure seamless integration with your tech stack:

• Shopify Payments: Fully integrated into Shopify, working with POS systems and accounting tools.
• Third-party PSPs: Requires setup (e.g., apps or APIs).

Test compatibility before committing.

5. Customer support

Reliable support is essential:

• Shopify Payments: 24/7 support via Shopify’s merchant team.
• Third-party PSPs: Support quality varies research reviews before choosing.

6. Scalability and flexibility

Your processor should grow with your business:

• Shopify Payments: Scales seamlessly within Shopify’s ecosystem.
• Third-party PSPs: Often designed for large-scale operations but may incur higher costs due to Shopify’s fees.

7. User experience (UX)

A smooth checkout process boosts conversions:

• Shopify Payments: Offers a unified, branded checkout experience.
• Third-party PSPs: Provides customizable checkout options to match your brand.

Test on multiple devices (desktop, mobile) to ensure usability.

8. Settlement time frames

Faster settlements improve cash flow:

• Shopify Payments: Typically deposits funds within 2–3 business days.
• Third-party PSPs: Varies by providersome take longer.

Compare settlement times to align with your financial needs.

9. Client reviews

Real-world feedback reveals strengths and weaknesses:

• Research reviews from businesses similar to yours.
• Focus on features like payment processing, fraud prevention, and customer support.

Extra tips

• International payments: Choose a processor that supports multiple currencies and local payment methods if targeting global markets.
• Reporting features: Look for comprehensive analytics tools to track sales trends and customer behavior.
• Customizable checkout: A branded checkout experience can reduce cart abandonment.
• Multi-location support: If you operate multiple stores, ensure the processor supports individual reporting and location-specific settings.

Make the right choice for your business

Choosing the right payment processor is a decision that can significantly impact your business’s profitability and customer experience. 

Key takeaways

1. Shopify Payments simplifies operations:
   No additional transaction fees, seamless integration, and unified reporting make Shopify Payments a cost-effective solution for most merchants.
2. Third-party PSPs offer flexibility but come with costs:
   While platforms like Mollie and Multisafepay provide advanced features and localized payment methods, Shopify charges an extra 0.6%–2% for using them. These hidden costs can add up quickly, especially for high-volume stores.
3. Evaluate your needs:
   Consider factors like supported payment methods, fee structures, security compliance, and scalability to ensure your choice aligns with your business goals.
4. Stay informed and test thoroughly:
   Regularly review Shopify’s policies and test your chosen processor to ensure it meets your needs without introducing unnecessary complexity or costs.

Final thoughts

For most businesses, Shopify Payments offers a streamlined, cost-effective solution that eliminates hidden fees and simplifies operations. However, if your business requires specialized tools or localized payment methods, carefully weigh the benefits of third-party PSPs against their additional costs. As an ecommerce agency that helps Shopify Plus merchants stress-test exactly this kind of payment-stack decision, we know how quickly overlooked fees can erode the flexibility third-party PSPs promise. Need expert help? Partner with Flatline Agency, your trusted Shopify Plus Partner, to find the best payment solution for your business.