If you're building an online store and trying to figure out which payment solution is right for your business, the Shopify Payments vs Stripe debate is one of the first decisions you'll face — and one of the most consequential.
On the surface, the two seem nearly identical. Shopify Payments is, in fact, powered by Stripe's infrastructure under the hood. Both accept major credit cards, both support digital wallets, and both are trusted by millions of businesses worldwide.
But for global small and medium-sized businesses (SMBs), the differences between them are significant — and choosing the wrong one can cost you in fees, lost sales, and unexpected account disruptions.
In this blog, we break down the Shopify Payments vs Stripe comparison across the factors that matter most to SMBs: fees, geographic availability, setup, checkout experience, and flexibility.
And we'll show you why Prosperna — which integrates Stripe directly — is increasingly the smarter choice for the best payment gateway for global SMBs who want the power of Stripe without the platform restrictions.
First, What's the Difference Between Shopify Payments and Stripe?
This is a question that trips up a lot of merchants — and understandably so. Here's the simplest way to think about it:
Stripe is a global payment infrastructure company. It provides the backend technology that processes card transactions for businesses of all sizes — including, notably, Shopify itself. Stripe operates independently and can be integrated into virtually any website, app, or platform.
Shopify Payments is Shopify's own branded payment gateway, built on top of Stripe's infrastructure. It's a white-labelled version of Stripe, designed exclusively for Shopify merchants.
When you use Shopify Payments, you're essentially using Stripe — but through Shopify's compliance layer, with Shopify's rules, restrictions, and geographic limitations applied on top.
Key insight: Using Shopify Payments means using Stripe's technology — but with Shopify's restrictions. Using Stripe directly (through a platform like Prosperna) gives you the same infrastructure with significantly more flexibility and fewer geographic limitations.
This distinction is what makes the Shopify Payments vs Stripe comparison so important for global SMBs. You're not just comparing two payment processors — you're comparing two very different levels of control over how you get paid.
Shopify Payments vs Stripe: The 6 Differences That Matter for SMBs
1. Geographic Availability
This is the most significant difference for global merchants.
Shopify Payments is available to merchants registered in approximately 23–25 countries — primarily in North America, Western Europe, Australia, Singapore, and a handful of other markets. If your business is registered outside these regions, Shopify Payments simply isn't available to you.
Stripe, on the other hand, supports merchants in 46+ countries — including many markets where Shopify Payments is unavailable. For SMBs in the Philippines, across Southeast Asia, in parts of Latin America, or across many African markets, Stripe is often accessible where Shopify Payments is not.
This alone makes Stripe the more viable option for a truly global SMB.
2. Transaction Fees and Hidden Costs
Here's where things get particularly important for SMBs managing tight margins.
Shopify Payments charges 2.9% + $0.30 per transaction on the Basic plan, dropping to 2.6% on the Shopify plan and 2.4% on Advanced — with no additional platform fee when you use Shopify Payments.
Stripe's standard rate is 2.9% + $0.30 per online transaction. Sounds identical — but the catch is what happens when you use Stripe on Shopify.
Because Stripe is a third-party gateway on Shopify's platform, Shopify charges an additional 0.5% to 2% surcharge on every transaction, on top of Stripe's processing rate. For an SMB doing $5,000 a month in revenue, that extra 2% surcharge alone adds up to $1,200 a year in avoidable costs.
The smarter path: When you use Stripe through Prosperna instead of Shopify, you pay only Stripe's standard processing rate — no additional platform surcharge. This is one of the most direct cost advantages of choosing Prosperna over Shopify for SMBs who need Stripe's global reach.
3. Country and Currency Support for Customers
Both platforms support international customers — but with different levels of flexibility.
Shopify Payments can display prices in multiple currencies through its Shopify Markets feature, but funds often settle back into your base currency, which introduces conversion costs. Currency conversion on Shopify Payments typically adds 1.5% for non-local currencies.
Stripe supports 135+ currencies natively, with more flexible settlement options and broader support for local payment methods — bank redirects, digital wallets, and regional card networks — depending on your region.
For SMBs selling across multiple markets, Stripe's currency and payment method depth is a meaningful advantage.
4. Platform Lock-In
Shopify Payments works exclusively within Shopify's ecosystem — and only on Shopify, Instagram, and Facebook storefronts. If you ever decide to migrate to a different eCommerce platform, you lose access to Shopify Payments entirely and must start over with a new payment setup.
Stripe is platform-agnostic. Your Stripe account, payment history, customer data, and settings travel with you regardless of which platform you're selling on.
This is a significant flexibility advantage for SMBs who may want to evolve their tech stack over time — or who are evaluating whether to move away from Shopify.
5. Checkout Experience
Shopify Payments comes bundled with Shop Pay — an accelerated one-tap checkout that Shopify reports can outperform standard guest checkout conversion by up to 50%. This is a genuine advantage for merchants in markets where Shop Pay has strong adoption, particularly in the US.
For global SMBs, though, Shop Pay's conversion advantage is less consistent.
In Southeast Asia, Africa, and Latin America, Shop Pay adoption is low, and local payment preferences often differ significantly. Stripe's checkout — particularly through Prosperna — supports Apple Pay, Google Pay, Link, and a range of local methods, which may resonate better with international audiences.
6. Account Stability and Compliance
Because Shopify Payments adds its own compliance layer on top of Stripe, it comes with stricter and sometimes less predictable account stability.
Merchants in certain product categories, those experiencing sudden sales spikes, or those with chargeback rates above 1% can find their Shopify Payments account suspended without warning — even if the same account would remain in good standing on standalone Stripe.
Using Stripe directly — through a platform like Prosperna — removes that additional compliance layer. You still operate within Stripe's own policies, but you're not subject to Shopify's additional restrictions, automated flags, or geographic eligibility requirements.
Quick Comparison: Shopify Payments vs Stripe via Prosperna
Merchant countries supported
Shopify Payments: ~23–25 countries. Not available in most of Southeast Asia, Africa, Latin America.
Stripe (via Prosperna): 46+ countries. Available in many markets where Shopify Payments is not.
Transaction fees on a Shopify store
Shopify Payments: 2.4%–2.9% + $0.30 with no platform surcharge when used natively on Shopify.
Stripe (via Prosperna): 2.9% + $0.30 Stripe rate only — no additional platform surcharge when used via Prosperna.
Currency support
Shopify Payments: 130+ display currencies via Shopify Markets; 1.5% conversion fee for non-local currencies.
Stripe (via Prosperna): 135+ currencies natively supported; local payment methods available by region.
Platform flexibility
Shopify Payments: Shopify only. Cannot be used on other platforms or if you migrate your store.
Stripe (via Prosperna): Platform-agnostic. Stripe account travels with you regardless of platform.
Accelerated checkout
Shopify Payments: Shop Pay (strongest in US market). Bundled free with Shopify Payments.
Stripe (via Prosperna): Apple Pay, Google Pay, Link. Strong globally, especially in non-US markets.
Account suspension risk
Shopify Payments: Higher — Shopify's compliance layer adds additional triggers on top of Stripe's own policies.
Stripe (via Prosperna): Lower — no Shopify compliance layer; subject only to Stripe's standard policies.
Setup time
Shopify Payments: Minutes — built directly into Shopify Settings > Payments for eligible merchants.
Stripe (via Prosperna): 1–2 minutes on Prosperna — connect your Stripe account via Settings > Payments.
Why Prosperna Is the Best Payment Gateway for Global SMBs Who Need Stripe
The conclusion from the Shopify Payments vs Stripe comparison is clear: Stripe is the more globally capable payment infrastructure.
The problem for many SMBs is that accessing Stripe through Shopify comes with significant added cost and restriction.
Prosperna solves this.
As an all-in-one eCommerce platform built specifically for SMBs, Prosperna integrates Stripe directly — giving you full access to Stripe's global payment infrastructure without Shopify's surcharges, geographic gatekeeping, or compliance layer sitting on top.
This is why Prosperna has become the best payment gateway for global SMBs looking for a Stripe-powered checkout that's simple to set up, cost-effective to operate, and built for selling internationally from day one.
What you get with Prosperna + Stripe:
• Direct Stripe integration — no third-party surcharge, no Shopify platform fee
• 135+ currencies supported from day one
• Accept Visa, Mastercard, Amex, JCB, Apple Pay, Google Pay, and Link
• PCI-compliant with 3D Secure fraud protection built in
• Subscriptions, one-time purchases, and payment link support
• Unified dashboard — store and payments in one place, no reconciliation gap
• Setup in 1–2 minutes — beginner level, no developer required
• Available in all Stripe-supported countries — far broader than Shopify Payments
Don't Pay More for Less Flexibility
If the Shopify Payments vs Stripe comparison has made one thing clear, it's this: for global SMBs, Stripe is the more capable and more globally accessible payment infrastructure. The only question is how you access it — and whether you want to pay Shopify's surcharges and operate under its restrictions to do so.
Prosperna gives you Stripe directly, with no platform tax, no geographic gatekeeping, and no added compliance layer. If you're building for global customers and want a payment experience that works as hard as your business does, it's worth a look.
Try Prosperna free — and access Stripe's full global power, without the Shopify surcharge.
Frequently Asked Questions
1. Is Shopify Payments the same as Stripe?
Not exactly. Shopify Payments is built on Stripe's infrastructure — it uses Stripe's technology to process transactions. But it operates under Shopify's compliance layer, with Shopify's geographic restrictions and account policies applied on top. Using Stripe directly gives you the same core technology with significantly more flexibility and broader country support.
2. Can I use Stripe on Shopify?
Yes, but Shopify charges an additional platform fee of 0.5%–2% (depending on your plan) on every transaction processed through Stripe as a third-party gateway. This surcharge is waived only when you use Shopify Payments natively. Using Stripe through a platform like Prosperna avoids this surcharge entirely.
3. Which is better for global SMBs — Shopify Payments or Stripe?
For global SMBs — especially those in countries where Shopify Payments isn't available — Stripe is the more capable and accessible choice. It supports 46+ merchant countries vs. Shopify Payments' ~23–25, offers 135+ currencies, and has broader local payment method support. The key is accessing Stripe through a platform that doesn't add surcharges on top, like Prosperna.
4. Does Prosperna charge extra for using Stripe?
No. Unlike Shopify, Prosperna does not charge an additional platform transaction fee for using Stripe as your payment gateway. You pay only Stripe's standard processing rate, making it a more cost-effective choice for SMBs who need Stripe's global capabilities.
5. What payment methods does Stripe support on Prosperna?
Depending on your region and Stripe account setup, you can accept Visa, Mastercard, American Express, JCB, Apple Pay, Google Pay, and Link. Local payment methods like bank redirects may also be available in supported regions. Stripe supports 135+ currencies, making it suitable for SMBs serving international customers.
Final Thoughts
The Shopify Payments vs Stripe debate isn't really about which technology is better — under the hood, they share the same infrastructure. What it's really about is control, cost, and geographic access.
For SMBs selling primarily in the US or a small number of Shopify-supported markets, Shopify Payments offers a seamless, cost-efficient experience within the Shopify ecosystem.
But for global SMBs — those selling across Southeast Asia, Africa, Latin America, or any market where Shopify Payments isn't available — Stripe accessed directly is the stronger foundation.
And when it comes to accessing Stripe without paying Shopify's platform tax or operating under its restrictions, Prosperna is the platform built for exactly that.
Simple setup, no surcharges, 135+ currencies, and a unified dashboard that keeps payments and your store in one place. That's what the best payment gateway for global SMBs actually looks like in practice.
Prosperna, Your Partner to eCommerce Success
Prosperna is an all-in-one AI-powered eCommerce platform for SMBs, entrepreneurs, and content creators. Our mission is to empower 1 million businesses with simple and affordable software powered by AI.
We’re so passionate about helping small businesses succeed that we’re giving you full access to our powerful tools for 14 days, absolutely free. No commitments—just pure growth for your store.
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