A deep dive in Shopify's pricing structure: Shopify Payments & transaction fees
If you’ve already read Part 1 of this series (our deep dive into Shopify’s Plans), you know that the monthly subscription fee is just the beginning. When it comes to the real cost of running a Shopify store, transaction fees are where things get interesting. This article breaks down how Shopify Payments actually works, why Shopify pushes merchants toward it, how fees differ per plan, and what happens if you stick with PayPal, Mollie, Stripe, or any other third-party provider.
First things first: what are transaction fees?
Every time someone pays on your store, a small percentage of the transaction goes to your payment provider. Think of it as the operational cost of moving money around: credit card networks, banks, fraud checks, chargeback protection, and so on.
On Shopify, you have two types of fees to consider:
- Credit card processing fees: charged by the payment processor.
- Additional Shopify transaction fees: only apply if you don’t use Shopify Payments.
That second part is where most merchants get confused. Let’s make it simple.
Shopify Payments: Shopify’s Native Payment Processor
Shopify Payments is Shopify’s built-in payment solution. If you activate it, you’ll pay only one fee: the standard credit card processing fee, which varies depending on your Shopify plan. No extra charges, no other hidden fees.
Why? Because Shopify strongly prefers that you use their native processor. It keeps more of the revenue within Shopify’s ecosystem and reduces support complexity.
The problem is: these small differences become meaningful very quickly as your volume grows.
What if you use a third-party processor?
If you prefer a third-party processor, such as Mollie, Stripe, PayPal,... your provider charges its fee plus Shopify adds an extra transaction fee for not using their native service.
Typical extra Shopify fees are Basic (+2%), Shopify (+1%) and Advanced (+0,5%). And that's in addition to whatever the chosen external provider charges.
One exception: Shopify Plus
If you’re on Shopify Plus, things get more flexible, because Plus merchants are able to negotiate their own Shopify Payments rate.
If they also want to use a third-party provider (e.g. for certain payment types or countries), Shopify waives the extra transaction fees, as long as Shopify Payments remains the primary checkout option.
This is one of the reasons enterprise merchants often switch to Plus, purely for cost optimization.
A quick overview of the Shopify transaction rates for the most used payment methods:
So… should you use Shopify Payments?
Often, it will be the most cost-efficient option. Here’s why:
- Lowest total cost (no extra Shopify fees)
- Smoothest checkout flow
- Best fraud protection + dispute management
- Instant integration and no technical overhead
- Works seamlessly with Shop Pay (which increases conversion rate)
But that doesn’t mean third-party providers are bad. You might choose them for:
- Local payment methods not in Shopify Payments
- Better rates in specific regions
- Existing long-term contracts
- Compatibility with complex ERP or accounting setups
Just know that the extra surcharge can eat into your margins fast.
Find out what you would pay!
Download our free Shopify Pricing Sheet and calculate your actual cost per order, across all Shopify plans, including Plus.
It’s the fastest way to understand whether Shopify Payments is the best deal for you, how fees change with your volume and where you can save thousands per year
Download the pricing sheet and get full clarity.
