Shopify Payments vs Stripe vs PayPal (2026): Which Payment Provider Is Right For Your Ecommerce Store?
TL;DR: I've been running a Shopify store since late 2024 and Shopify Payments has been my payment provider from day one. Here's the honest breakdown - and why Shopify Payments is the obvious choice for most serious ecommerce store owners.
Payment Providers Matter More Than You Think
Most ecommerce store owners spend weeks choosing their platform, their theme and their apps.
Then they spend five minutes choosing their payment provider.
That's a mistake.
Your payment provider affects your checkout conversion rate, your fees, your cash flow and how much time you spend managing your finances. Choosing the wrong one costs you money every single day.
If you're not on Shopify yet - read why I switched from WordPress to Shopify and what happened to my revenue.
The Honest Framing
I use Shopify Payments. I have since day one.
I haven't used Stripe or PayPal as primary payment providers personally. But after running a Shopify store for over a year and a half - and seeing how Shopify Payments continues to develop - I don't need to.
Here's why.
Shopify Payments: The All-In-One Solution
Shopify Payments is Shopify's built-in payment provider. It's fully integrated into your store from day one - no separate account, no extra integration, no third party dashboard to manage.
The reason I chose Shopify Payments and haven't looked back is simple:
Everything is in one place.
- Setup takes minutes
- No separate account needed
- All payouts land in one dashboard
- No additional transaction fees on top of your Shopify subscription
- Your orders, payments and payouts are all visible in the same place
There's no back and forth between platforms. No separate logins. No reconciling data from multiple sources. Everything your store does financially is visible in one clean dashboard.
For a store owner who wants to focus on selling rather than managing tools - that's genuinely valuable.
Shopify Payments Keeps Getting Better
What makes Shopify Payments stand out is that it's not standing still.
Shopify continuously develops and expands the platform - and the payment integrations reflect that.
MobilePay is now integrated into Shopify Payments in Denmark. If you're selling to Danish customers this is significant. MobilePay is the dominant mobile payment method in Denmark - not having it at checkout means losing sales. Having it built directly into Shopify Payments means zero extra setup.
Klarna is available as a Shopify integration for Swedish and Nordic markets where buy-now-pay-later is extremely popular. While not directly part of Shopify Payments it integrates cleanly with your Shopify checkout.
This is the pattern with Shopify - they keep adding the payment methods your customers actually use. You don't need to chase integrations yourself.
What Shopify Payments does well:
- Instant setup - no separate account needed
- Fully integrated into your Shopify dashboard
- All payouts in one place
- No additional transaction fees when used as your primary provider
- Supports major credit cards, Apple Pay, Google Pay
- MobilePay integration for Danish market ✅
- Chargeback management built in
- Automatically syncs with your Shopify orders and analytics
- Continuously expanding payment method support
What Shopify Payments doesn't do as well:
- Only available in select countries
- Can be more expensive than local providers like PensoPay at very high volumes
- If Shopify freezes your account your payments are frozen too
Shopify Payments is the right choice if:
You're running a Shopify store and want everything in one place. For most Shopify store owners - this is the obvious starting point.
Get started with Shopify Payments:
Stripe: Powerful But Complex
Stripe is one of the most powerful payment infrastructure platforms in the world. It powers payments for some of the biggest companies globally and offers an almost unlimited level of customization.
What Stripe does well:
- Extremely powerful and flexible
- Works with virtually any platform
- Excellent developer tools and API
- Supports payments in 135+ currencies
- Advanced fraud detection
- Highly customizable checkout
What Stripe doesn't do as well:
- Requires significantly more setup than Shopify Payments
- Separate dashboard from your Shopify store
- Additional transaction fees when used alongside Shopify Payments
- More complexity than most ecommerce store owners need
- Support can be slow for smaller businesses
Stripe is the right choice if:
You need maximum flexibility - for example a custom built store or a complex multi-channel operation. For standard Shopify stores the added complexity rarely justifies moving away from Shopify Payments.
PayPal: The Trust Builder - But With Limitations
PayPal is the most recognized payment brand in the world. Billions of people have a PayPal account and many prefer to pay with it - especially for their first purchase from an unknown store.
What PayPal does well:
- Massive global brand recognition and trust
- Billions of active users worldwide
- Good for international payments
- Works well as a secondary payment option
What PayPal doesn't do as well:
- Higher fees than most alternatives
- Frequent account freezes and holds - especially for newer stores
- Separate dashboard from your Shopify store
- Customer service is notoriously difficult
- Not recommended as a standalone primary payment provider
PayPal is the right choice if:
You add it as a secondary option alongside Shopify Payments to capture customers who specifically prefer PayPal at checkout. Not as your primary provider.
The Honest Comparison
Pricing: What You Actually Pay
Pricing depends on your location, your Shopify plan and your volume.
See current Shopify Payments pricing:
A Note For Danish Store Owners
If you're based in Denmark and running high volumes - local providers like PensoPay can be more cost effective than international providers at scale.
That said - for most Danish Shopify store owners Shopify Payments remains the simplest and most integrated option. The MobilePay integration alone makes it the obvious starting point for the Danish market.
We'll cover Danish payment providers including PensoPay in a separate post.
Which One Is Right For You?
Choose Shopify Payments if:
- You're running a Shopify store
- You want everything in one dashboard
- You sell to Danish customers and need MobilePay
- Simplicity and integration matter to you
- You want a payment provider that keeps developing
Consider adding Stripe if:
- You need maximum flexibility and customization
- You're running a custom built or multi-platform store
Add PayPal as a secondary option if:
- You want to capture customers who specifically prefer PayPal
- You sell internationally where PayPal trust is high
The Bottom Line
Stripe is powerful. PayPal is globally recognized.
But for Shopify store owners there's really only one obvious starting point - and that's Shopify Payments.
Setup takes minutes. Everything is in one dashboard. All payouts in one place. MobilePay built in for Danish customers. And Shopify keeps adding the payment methods your customers actually want to use.
I've been using it since day one and haven't felt the need to look elsewhere.
If you're serious about ecommerce - start with Shopify and let Shopify Payments handle the rest.
Start with Shopify.
Have questions about which payment provider is right for your store? Feel free to reach out.
Frequently Asked Questions
Is Shopify Payments better than Stripe?
For Shopify store owners - yes in most cases. Shopify Payments is fully integrated into your dashboard, requires no extra setup and avoids additional transaction fees. Stripe is more powerful for custom built stores that need maximum flexibility.
Can I use PayPal with Shopify Payments?
Yes. You can use both at the same time. Many store owners use Shopify Payments as their primary provider and add PayPal as a secondary option to capture customers who prefer paying with PayPal.
Is MobilePay available on Shopify?
Yes. MobilePay is integrated into Shopify Payments in Denmark - making it one of the strongest reasons for Danish store owners to choose Shopify Payments as their primary provider.
Is Klarna available on Shopify?
Yes. Klarna is available as a Shopify integration - particularly popular for Swedish and Nordic markets where buy-now-pay-later is widely used.
Does Shopify charge extra fees if I use Stripe or PayPal?
Yes. If you use a third party payment provider instead of Shopify Payments Shopify charges an additional transaction fee. Using Shopify Payments avoids this entirely.
What is the cheapest payment provider for Shopify?
It depends on your volume and location. Shopify Payments avoids Shopify's additional transaction fees making it cost effective for most store owners. At very high volumes local providers like PensoPay can become more competitive.
Get started. Don't think - just start.
Is Shopify Payments available in Denmark?
Yes. Shopify Payments is available in Denmark and includes MobilePay integration - making it the obvious choice for Danish ecommerce store owners.
Ready to get started with Shopify Payments?
