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- Considering switching from PensoPay or QuickPay to native Shopify Payments, or vice versa
- Unsure if the difference in fees is actually large enough to make a switch worth the effort
- Have experienced confusion at checkout due to duplicate card payment options
- Want to understand how payout speed and cash flow factor into the decision
Historically, one of the clearest reasons to choose a third-party provider like PensoPay or QuickPay has been MobilePay support, as Shopify Payments did not support it natively. That has changed: Shopify Payments now supports MobilePay directly, without requiring an external gateway.
This means that the decision regarding a payment provider today is more about fees, payout speed, and support, rather than which provider can offer MobilePay. If you previously chose a third-party provider specifically for that reason, it is worth reconsidering whether that reason is still valid.
How to compare fees correctly
The most common mistake is comparing providers' advertised percentages directly without accounting for the full, actual fee structure. A fee that looks lower on the surface can end up being more expensive in practice once fixed monthly fees, transaction surcharges, and any additional platform fees are added up.
The right approach is to find the actual blended fee rate—the total percentage of revenue that truly goes toward payment processing once all fees are included. This rate can be found directly in Shopify under Settings → Payments → View payouts, where the actual blended rate for your current setup is displayed.
With the actual rate in hand, you can convert potential savings or additional costs into something concrete and understandable: a fee difference of less than 1 percentage point, for example, might mean that your conversion rate only needs to increase from 2.00% to 2.027% to break even—a very small, often achievable margin if you are also working on conversion rate optimization.
Fees are not the only factor to consider. Payout speed has a direct impact on cash flow, especially for growing brands that quickly reinvest revenue into inventory or advertising.
Native Shopify Payments typically offers daily, rolling payouts. Third-party providers may have longer or more variable settlement cycles, depending on the setup and agreement. For a brand that relies on quick access to liquidity, a slower payout cycle can, in practice, outweigh a minor fee advantage, even if the third-party provider is technically cheaper on paper.
An often-overlooked detail when running a third-party provider alongside other payment methods is the risk of the customer seeing two different card payment options at checkout—one from Shopify and one from the third-party provider. This creates confusion and can, in itself, cost you conversions because the customer is unsure which option to choose.
Before activating a new payment provider, you should therefore always test the checkout as a new customer to ensure that only one clear option is displayed per payment type, rather than a duplicate solution that leaves room for doubt.
Switching is not always the right decision, even if Shopify Payments looks cheaper in theory. There are situations where it makes more sense to stay:
- The fee difference is small, and your current provider offers strong, local support, the value of which is hard to underestimate.
- You have a well-functioning integration or agreement where the cost of switching (time, testing, risk of errors during the transition) outweighs the potential savings.
- The payout speed of your current provider is already sufficient for the company's cash flow needs.
If the fee difference is minimal and your current solution is working well, it is often not worth the effort to switch for a marginal saving.
Moving from uncertainty to a clear decision requires a solid process:
1. Find the actual blended fee rate for your current setup
Go to Settings → Payments → View payouts in Shopify and identify the actual percentage that goes toward payment processing.
2. Compare against Shopify Payments' full fee structure
Include all relevant fees — not just the most visible percentage — for both options.
3. Translate the difference into something concrete
Translate the fee difference into what it means in practice: a marginal increase in conversion rate or a specific monetary difference per order.
4. Evaluate payout speed and support as part of the calculation
A small fee saving can quickly become irrelevant if it costs you in cash flow or support quality.
1. Does Shopify Payments support MobilePay now?
Yes, Shopify Payments has supported MobilePay directly since a platform update in 2025, without requiring an external payment provider.
2. How do I find the actual fee rate for my current payment provider?
Go to Settings → Payments → View payouts in your Shopify admin, where the actual blended fee rate for your setup is displayed.
3. Is Shopify Payments always cheaper than PensoPay or QuickPay?
Not necessarily. It depends on your specific fee structure, transaction volume, and the additional services (such as local support) that your current provider offers.
4. What is the risk of running multiple payment providers simultaneously?
The most common risk is duplicate card payment options at checkout, which can confuse the customer and potentially cost you conversions.
5. When is it not worth switching payment providers?
When the fee difference is minimal and your current provider offers strong support or sufficient payout speed that would be lost or diminished by switching.
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