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Choosing the right payment gateway isn’t just a technical decision anymore. In 2026, payments directly influence conversion rate, checkout speed, customer trust, and scalability.
For UK eCommerce brands on Shopify, the comparison usually comes down to Mollie vs Shopify Payments.
Both are strong options. But they solve very different problems.
This guide breaks down fees, checkout experience, scalability, and real-world use cases, so you can choose the payment setup that actually supports growth not friction.
What Is Mollie?
Mollie is a European payment service provider headquartered in the Netherlands. It enables online businesses to accept a wide range of payment methods, including:
- Credit & debit cards
- PayPal
- Klarna
- iDEAL
- SEPA Direct Debit
Mollie is platform-agnostic, meaning it works across Shopify, WooCommerce, BigCommerce, and custom builds.
Its biggest strengths are local payment coverage, simplicity, and clean reporting.
What Is Shopify Payments?
Shopify Payments is Shopify’s native payment gateway, built directly into the Shopify platform.
It supports:
- Visa, Mastercard, Amex
- Apple Pay & Google Pay
- Shop Pay (accelerated checkout)
- Local payment methods by region
There’s no third-party setup, no external dashboard, and no redirected checkout.
For Shopify merchants, it removes an entire layer of complexity.
Mollie vs Shopify Payments: Key Differences That Matter in 2026
1. Checkout Experience & Conversion Rate
Checkout friction is one of the biggest silent revenue killers.
Shopify Payments
- Fully native checkout
- No redirects
- Faster page loads
- Supports Shop Pay, one of the highest-converting checkouts globally
Mollie
- Can introduce external payment steps depending on method
- More flexibility, but more friction
- Slightly slower checkout flow
For high-volume DTC brands, native checkout almost always outperforms redirected flows in conversion testing.
Winner: Shopify Payments
2. Fees & Cost Transparency (UK)
Costs vary by plan and payment method, but the structure matters.
Shopify Payments
- No extra Shopify transaction fees
- Card processing rates tied to Shopify plan
- Fewer surprise costs at scale
Mollie
- Pay-per-transaction pricing
- Fees differ by payment method
- Can become harder to forecast as order volume grows
For merchants processing high volumes, predictability often matters more than marginal per-transaction differences.
Winner: Shopify Payments (for scale)
3. Platform Compatibility & Flexibility
Mollie
- Works across multiple platforms
- Strong choice for hybrid or non-Shopify stacks
Shopify Payments
- Shopify-only
- Deeply integrated, but not portable
If Shopify is your core platform, portability usually isn’t a concern.
Winner: Mollie (for multi-platform brands)
4. Reporting, Operations & Admin Efficiency
Shopify Payments
- Unified reporting inside Shopify admin
- Orders, payments, refunds, and chargebacks in one place
- Easier finance and ops workflows
Mollie
- Separate dashboard
- More reconciliation steps for teams
- Additional tooling often required at scale
Operational simplicity compounds as brands grow.
Winner: Shopify Payments
5. Fraud Protection & Trust Signals
Shopify Payments
- Built-in fraud analysis
- Automatic risk scoring
- Trusted checkout UX
Mollie
- Fraud tools available
- Often requires additional configuration
For UK customers, familiar checkout flows directly impact trust.
Winner: Shopify Payments
When Mollie Makes Sense
Mollie is a strong option if:
- You operate across multiple eCommerce platforms
- You rely heavily on specific European payment methods
- You need payment flexibility outside the Shopify ecosystem
It’s not a bad choice it’s just not optimised for Shopify-first growth.
When Shopify Payments Is the Better Choice
Shopify Payments is ideal if:
- Shopify is your primary sales channel
- Conversion rate matters more than configurability
- You want faster checkout and cleaner ops
- You’re scaling order volume in the UK or internationally
For most Shopify Plus and high-growth DTC brands, this is the default recommendation.
Common Mistakes Brands Make with Payments
From WIRO audits, the most common issues we see:
- Choosing gateways based on fees alone
- Ignoring checkout friction and redirects
- Overcomplicating payment stacks unnecessarily
- Failing to test conversion impact properly
Payments should support growth not quietly cap it.
WIRO’s Take: Payments Are a Growth Lever, Not a Plugin
At WIRO, we treat payments as part of the conversion system, not just infrastructure.
We help brands:
- Audit checkout performance
- Reduce friction across payment flows
- Align gateways with growth stage
- Optimise Shopify Payments for higher conversion and AOV
For most Shopify brands we work with, Shopify Payments delivers the strongest long-term ROI.
Final Verdict: Mollie vs Shopify Payments
There’s no universal winner but there is a smarter default.
- Multi-platform or niche payment needs? Mollie
- Shopify-first, scaling brand? Shopify Payments
If your goal is speed, simplicity, and conversion growth, Shopify Payments is usually the better long-term choice.
Want Help Choosing or Optimising Your Payment Setup?
If you’re unsure which gateway fits your growth stage or want to test, optimise, and improve checkout performance that’s exactly what we do.
