Shopify Payments vs third-party PSPs: "Hidden" costs and fees you need to know (2026)

Imagine this: you’ve spent months perfecting your Shopify store, optimizing product pages, crafting marketing campaigns and fine-tuning your checkout. But what if a fee you never noticed was quietly eating into your margin?

Choosing the right payment processor is one of the most important decisions for any Shopify merchant. Providers like Mollie, MultiSafepay and Pay.nl offer flexibility and extra features, but there is a catch: Shopify charges an additional transaction fee on every order you process through a third-party provider instead of its own solution, Shopify Payments. Those costs add up quickly and come straight out of your margin.

In this guide we compare Shopify Payments with third-party Payment Service Providers (PSPs), show the current fees per plan, uncover the costs merchants often overlook and help you make the right decision for your business.

All rates in this article are Shopify’s published rates for stores based in the Netherlands, as of September 2026. Rates differ per country and can change, so always check the current Shopify pricing page.

What is Shopify Payments?

Shopify Payments is Shopify’s native payment solution, built directly into the platform. You activate it from your Shopify admin, without a separate contract with an external payment provider, and you manage payments in the same place as your orders.

How does Shopify Payments work?

Shopify Payments acts as payment processor and merchant account in one. Behind the scenes, Shopify works with licensed payment processors: according to Shopify’s own list of payment processors for Shopify Payments, those are Stripe Payments Europe and Adyen for countries such as the Netherlands, Belgium and Germany. As a merchant, you only deal with Shopify: one admin, one payout and one set of rates.

Here’s a breakdown of how Shopify Payments works:

1. Customer initiates payment: the customer picks a payment method at checkout, such as a credit or debit card, iDEAL, Bancontact, Klarna or a wallet like Apple Pay.

2. Transaction processing: Shopify Payments transmits the payment data securely through Shopify’s checkout.

3. Authorization and authentication: the payment is verified and approved by the customer’s bank or the payment method provider.

4. Completion of payment: once approved, the funds are paid out to your bank account on your Shopify Payments payout schedule, without a separate merchant account or external processor. For details, see Shopify’s help center on Shopify Payments.

Key benefits of Shopify Payments

• No third-party transaction fee: Shopify does not charge its additional transaction fee on orders paid through Shopify Payments, Shop Pay, Shop Pay Installments or PayPal Express Checkout.

• Unified admin: orders, payments, payouts and chargebacks live in one place, which makes tracking and reconciliation easier.

• Local payment methods: for stores in the Netherlands, Shopify Payments supports iDEAL, Bancontact and Klarna next to cards, each with its own rate (see the tables below).

• Local currencies: showing prices in your customers’ local currency requires Shopify Payments.

• Built-in fraud analysis: included with Shopify Payments at no extra cost.

• PCI compliance: Shopify is certified PCI DSS Level 1 compliant, so your store meets PCI standards by default.

Shopify Payments fees per plan (as of September 2026)

These are Shopify’s published prices for a store based in the Netherlands. Subscription prices are per month; the lower price applies when you pay yearly.

Shopify Payments processing rates for online payments, per plan:

iDEAL and Bancontact have no percentage component: you pay 0% plus a fixed fee per transaction. Source: Shopify pricing page for the Netherlands, as of September 2026. Want the full picture, including apps and themes? Read our overview of Shopify costs.

Why choose Shopify Payments over third-party PSPs?

Third-party PSPs like Mollie, MultiSafepay and Pay.nl offer features and flexibility, but they come with a significant drawback: Shopify charges an additional transaction fee when you process payments through them instead of Shopify Payments. As of September 2026, that fee ranges from 0.2% (Plus) to 2% (Basic), depending on your plan, and it comes on top of what your PSP charges. For stores processing tens of thousands of euros a month, that adds up quickly.

With Shopify Payments you avoid that fee and get a payment solution that is built for Shopify: less setup, fewer moving parts and one place to manage orders and payments. You can read more on the official Shopify Payments page.

What are third-party PSPs?

Many merchants still choose a third-party Payment Service Provider (PSP) such as Mollie, MultiSafepay or Pay.nl. These providers bring flexibility and features that suit specific business needs. The trade-off is Shopify’s additional transaction fee on every order that runs through them.

What is a third-party PSP?

A third-party PSP is an external payment provider that you connect to Shopify, usually through a payments app. Unlike Shopify Payments, it operates independently, with its own contract, dashboard, rates and payouts. Examples include:

• Mollie: popular in the Benelux for its wide range of local payment methods and clear dashboard.

• MultiSafepay: Dutch PSP with a broad set of payment methods and fraud prevention tools.

• Pay.nl: Dutch PSP focused on local payment methods and flexible checkout options.

These providers handle a wide range of payment methods, from cards and wallets to bank transfers and buy now, pay later. They are especially popular with businesses that sell through several channels or platforms and want one payment contract for all of them.

Key features of third-party PSPs

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

1. Flexibility in payment methods: depending on the provider, you get access to payment methods that Shopify Payments does not offer in your market, such as specific gift cards or pay-later options like in3 or Riverty. Note that iDEAL, Bancontact and Klarna are no longer a reason on their own: Dutch stores can offer them through Shopify Payments.

2. Advanced features: many PSPs offer their own fraud rules, reporting, payment links and recurring payments, sometimes with more configuration options than Shopify Payments.

3. One provider across channels: if you also sell outside Shopify, for example on a second platform or in a separate B2B portal, one PSP keeps your payments and reconciliation in one place.

The catch: Additional transaction fees

When you use a third-party PSP, Shopify charges an additional transaction fee on every order processed through it. As of September 2026, the fee per plan is:

• Basic: 2%

• Grow (formerly the “Shopify” plan): 1%

• Advanced: 0.6%

• Plus: 0.2%

Shopify calculates this fee over the full order amount: product price minus discounts, plus tax, plus shipping, times the rate. It comes on top of your PSP’s own processing fees.

Example: a store that processes €50,000 a month through a third-party PSP pays Shopify an extra €100 to €1,000 a month, depending on the plan. Over a year, that is €1,200 to €12,000:

Example calculation based on Shopify’s rates as of September 2026, excluding your PSP’s own fees.

Why does Shopify charge these fees?

Shopify wants merchants to use Shopify Payments, which keeps payments, payouts and reporting inside the platform. According to Shopify, the third-party transaction fee covers the cost of providing a secure checkout and integrating with external payment providers. In practice, it makes Shopify Payments the cheapest choice for most stores.

Hidden costs that merchants often overlook

Many merchants only notice these fees once the first Shopify bill arrives. Points to watch:

• A merchant using Mollie on the Grow plan pays Mollie’s fees plus 1% to Shopify on every order. On a €100 iDEAL order, Shopify’s fee alone (€1.00) is more than three times the Shopify Payments iDEAL rate (€0.29).

• The fee is calculated over the full order amount, including tax and shipping, not just the product price.

• Shopify does not return third-party transaction fees when you refund an order.

• On stores created on or after 12 May 2025, Shopify also charges the fee on the part of an order paid with gift cards or store credit, even if you use Shopify Payments.

• On Plus, the fees are only waived if Shopify Payments is your only payment provider. Add a third-party PSP alongside it and transaction fees apply.

To avoid surprises, check Shopify’s official guide on third-party transaction fees before you decide.

When should you consider a third-party PSP?

Despite the additional fees, there are situations where a third-party PSP is the better choice:

1. Localized payment needs: your customers use payment methods that Shopify Payments does not support in your market.

2. Shopify Payments is not available: Shopify Payments is only available in certain countries and not for every type of business. In that case you need an external provider anyway.

3. Existing partnerships or negotiated rates: some merchants have a contract with Mollie or MultiSafepay with rates that, at high volume, can offset part of Shopify’s extra fee.

4. Multiple platforms: if you sell on several platforms, one PSP gives you a single view of all payments.

Always weigh these benefits against the extra costs. A practical test: your PSP has to be cheaper than Shopify Payments by at least Shopify’s transaction fee before it pays off on cost alone.

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

Both options have strengths and weaknesses. Below we compare them on the factors that matter most, so you can judge which one fits your store.

1. Integration complexity

• Shopify Payments: built into Shopify and activated from your admin, without extra apps or API work. Downside: less room for custom setups.

• Third-party PSPs (e.g. Mollie, MultiSafepay, Pay.nl): installed through a payments app, with a separate contract, dashboard and settings. More options, but also more maintenance and more to reconcile.

2. Transaction fees

• Shopify Payments: no additional Shopify transaction fee. You pay processing fees per payment method, which drop on higher plans. Standard online cards (as of September 2026): Basic 1.9% + €0.25, Grow 1.8% + €0.25, Advanced 1.6% + €0.25, Plus 1.4% + €0.25. iDEAL costs €0.29 per transaction (Plus: €0.15).

• Third-party PSPs: your PSP’s own rates plus Shopify’s additional fee: Basic 2%, Grow 1%, Advanced 0.6%, Plus 0.2%.

Example per order: on Grow, a €100 card payment through Shopify Payments costs €2.05 (1.8% + €0.25). Through a third-party PSP you pay Shopify €1.00, plus your PSP’s own fee. You only break even if that PSP fee is €1.05 or less.

3. Supported regions and payment methods

• Shopify Payments: available in a growing but limited list of countries, with local methods such as iDEAL, Bancontact and Klarna for Dutch stores, and multi-currency selling. Not every niche or regional payment method is supported.

• Third-party PSPs: Mollie, MultiSafepay and Pay.nl are strong in European payment methods and sometimes offer methods that Shopify Payments doesn’t. Downside: Shopify’s additional fee on every order.

4. Unique features

• Shopify Payments: built-in fraud analysis, Shop Pay, local currency display and unified reporting in your Shopify admin. Downside: fewer configuration options than some specialized PSPs.

• Third-party PSPs: often extras like payment links, recurring payments, custom fraud rules and detailed reporting. Downside: higher costs because of Shopify’s fee.

5. Security compliance

Both Shopify Payments and third-party PSPs comply with PCI DSS (Payment Card Industry Data Security Standard). Shopify is certified PCI DSS Level 1 compliant and handles security within its checkout. With a third-party PSP, check how the provider handles compliance and what you need to arrange yourself.

6. Settlement time frames

• Shopify Payments: payouts follow a fixed payout schedule. How fast depends on your country and account; you can see your schedule in your Shopify admin.

• Third-party PSPs: settlement times differ per provider and contract. Some offer faster payouts, sometimes for an extra fee.

7. Customer support

• Shopify Payments: support through Shopify, the same team that supports your store.

• Third-party PSPs: support through the PSP. Quality varies per provider, and for issues between Shopify and your PSP you may have to deal with two parties.

8. Scalability and flexibility

• Shopify Payments: rates drop on higher plans, down to 1.4% + €0.25 for standard online cards on Plus.

• Third-party PSPs: built for large volumes and often open to negotiated rates, but Shopify’s fee grows in line with your revenue.

Comparison table: Shopify Payments vs. third-party PSPs

Shopify rates for stores in the Netherlands, as of September 2026. Source: Shopify pricing page.

Factors to consider when choosing a payment processor

Choosing the right payment processor matters for your margin and your conversion. Here are nine factors to help you decide between Shopify Payments and a third-party PSP like Mollie, MultiSafepay or Pay.nl:

1. Supported payment options

Know how your customers want to pay. In the Netherlands, iDEAL is the most used online payment method; in Belgium, it’s Bancontact; elsewhere, cards, wallets like Apple Pay or buy now, pay later. Check whether Shopify Payments supports the methods your market expects. For Dutch stores, iDEAL, Bancontact and Klarna are available. Only if you need methods beyond that does a third-party PSP become necessary.

2. Fee structures

Cost matters. Compare fees carefully:

• Shopify Payments: no additional Shopify fee; processing fees per payment method and plan.

• Third-party PSPs: the PSP’s own fees plus Shopify’s additional 0.2% to 2%.

Calculate the total cost per order based on your own payment mix, not just the headline card rate.

3. Security compliance

Both options meet PCI DSS. Shopify Payments handles security within the checkout; with a third-party PSP, check what the provider covers and what you arrange yourself. Also look at fraud detection and how 3D Secure is handled.

4. Compatibility

Make sure the processor fits your tech stack:

• Shopify Payments: works directly with Shopify checkout, POS, Markets and reporting.

• Third-party PSPs: run through a payments app; check compatibility with your ERP, accounting software and other Shopify integrations.

Test the full flow, including refunds and reconciliation, before you commit.

5. Customer support

Reliable support is essential:

• Shopify Payments: support through Shopify.

• Third-party PSPs: quality varies per provider, so read reviews before you choose.

6. Scalability and flexibility

Your processor should grow with your business:

• Shopify Payments: lower rates on higher plans, up to Plus.

• Third-party PSPs: suitable for large volumes, but Shopify’s fee grows in line with your revenue.

7. User experience (UX)

A smooth checkout supports conversion:

• Shopify Payments: payments run within Shopify checkout, including Shop Pay.

• Third-party PSPs: depending on the integration, customers may be redirected to the PSP’s payment page.

Test on desktop and mobile to make sure checkout works well.

8. Settlement time frames

Faster settlements improve cash flow:

• Shopify Payments: payouts on a fixed schedule that depends on your country.

• Third-party PSPs: varies by provider and contract.

Compare settlement times with your cash flow needs.

9. Client reviews

Real-world feedback shows strengths and weaknesses:

• Read reviews from businesses similar to yours.

• Focus on payment processing, fraud prevention and customer support.

Extra tips

• International payments: selling across borders? Check multi-currency support and local payment methods per market.

• Reporting features: make sure payouts and fees are easy to reconcile in your accounting.

• Checkout experience: every extra step or redirect can cost conversion.

• Multi-location support: with several stores or locations, check that reporting and settings work per location.

Make the right choice for your business

The right payment processor affects both your margin and your customers’ checkout experience. Base the decision on your own numbers: order volume, average order value and payment mix.

Key takeaways

1. Shopify Payments is the cheapest option for most stores: no additional Shopify fee, and Dutch stores can offer iDEAL, Bancontact and Klarna through it.

2. Third-party PSPs offer flexibility at a price: as of September 2026, Shopify charges 2% (Basic), 1% (Grow), 0.6% (Advanced) or 0.2% (Plus) extra on every order, on top of your PSP’s fees.

3. Evaluate your needs: look at payment methods, total cost per order, security, compatibility and scalability.

4. Check the rates regularly: Shopify adjusts plans and rates from time to time, so always check the current pricing page before you decide.

Final thoughts

For most businesses, Shopify Payments is the simplest and cheapest option. If you need specific payment methods or features, weigh the benefits of a third-party PSP against Shopify’s extra fee and do the math on your own volume.

As a Shopify agency and Shopify Platinum Partner in Amsterdam, Flatline Agency helps brands on Shopify Plus stress-test exactly this kind of payment-stack decision. Moving to Shopify from another platform? Our Shopify migration approach takes your payment setup into account from day one.