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Best Shopify Payment Gateways in 2025: A Guide for Global Shopify Sellers
If you’ve been researching e-commerce, you’ve probably seen the advice:
“Just use Shopify Payments and you’re all set.”
It sounds simple, but the reality is more complicated.
The truth is, choosing the best Shopify payment gateways in 2025 isn’t about clicking one button. It’s about balancing fees, availability, customer trust, and flexibility.
The wrong choice can quietly eat away at your profit margins or even block your store from selling in certain regions.
On the other hand, the right setup can reduce fees, build customer confidence, and give you access to payment methods your buyers already trust. Let’s dive into the global landscape and figure out what really works.
The Shopify Payments Myth
Shopify Payments is often marketed as the ultimate solution, and in many cases, it’s true.
It integrates seamlessly with your store, avoids extra third-party fees, and supports major credit cards, Apple Pay, and Google Pay.
For beginners, it feels like the easiest choice.
But here’s where things get tricky: Shopify Payments isn’t available in every country.
If you’re selling from regions like the UAE, Pakistan, or many parts of Africa, you’ll need to rely on third-party payment providers for Shopify.
Even in supported countries, industries like supplements, CBD, or high-risk digital products may be excluded. That’s why it’s essential to look beyond the default option.
What Makes the Best Payment Provider for Shopify?
When deciding which are the best Shopify payment gateways and is right for you, it’s not just about who charges the lowest fee. The best payment method for Shopify will depend on your market and model.
For example, transaction fees matter, but so do payout times. Shopify Payments typically pays within one to three business days, but some third-party providers may take a week or longer.
Before choosing between PayPal, Stripe, Klarna, Afterpay, or Shopify’s own solution, you need to know what actually matters:
- Transaction Fees & Shopify Payments Fees – Shopify typically charges 2.9% + 30¢ per transaction (lower on higher plans). If you don’t use Shopify Payments, expect an additional 0.5–2% fee.
- Availability by Country – Stripe and Shopify Payments aren’t global. Options like 2Checkout for Shopify also known as verifone now, serve 200+ countries.
- Payout Times – Cash flow matters. Shopify Payments pays in 1–3 business days. PayPal and Stripe vary.
- Recurring Payments – If you’re running a subscription box, not every gateway supports Shopify recurring payments.
- Fraud & Chargebacks – Every dropshipper dreads the word chargeback. Your gateway should offer strong fraud prevention.
- Customer Trust – Some customers only buy if they see PayPal. Others prefer BNPL options like Shopify Afterpay or Klarna for Shopify.
Best Shopify Payment Gateways in 2025
Let’s break down the options you’re most likely to consider.
Shopify Payments
For those in supported countries, Shopify Payments is still the most streamlined option. It reduces fees, integrates flawlessly, and allows you to accept all major credit cards without needing a separate merchant account. If it’s available to you, it should usually be your foundation.
Stripe
Stripe is one of the best third-party payment providers for Shopify because of its global coverage and flexibility. It’s especially powerful if you plan to run subscriptions, since it handles recurring billing better than most. That said, Stripe can be strict about what products you sell, so high-risk niches may face restrictions.
PayPal
When it comes to building customer trust, nothing beats PayPal. Millions of shoppers prefer it, and having PayPal available on your Shopify store can increase conversions almost instantly. The downside is higher dispute rates and the possibility of sudden fund freezes, so you’ll want a backup option.
Klarna and Afterpay
The rise of Buy Now, Pay Later has changed how people shop online. Klarna for Shopify and Afterpay for Shopify are perfect for fashion, lifestyle, and impulse-buy products. They let customers split payments into installments, often boosting average order value. The trade-off? Higher fees, typically between 4–6% per transaction.
2Checkout (Verifone)
If you’re based in a country where Shopify Payments or Stripe aren’t available, 2Checkout for Shopify is often the most reliable fallback. It works in over 200 countries, supports multiple currencies, and allows you to sell internationally. The downside is slightly higher fees compared to Shopify Payments.
Here’s the real breakdown of the top options, including fees, availability, and ideal use cases.
| Provider | Best For | Key Features | Fees |
| Shopify Payments | Beginners in supported countries | Seamless integration, no extra Shopify fee | 2.9% + 30¢ (varies by plan & country) |
| Stripe | Global reach & tech businesses | Wide payment options, recurring billing, supports 135+ currencies | 2.9% + 30¢ |
| PayPal | Customer trust & flexibility | Widely used, PayPal Credit, and buyer protection | 2.9% + fixed fee (country-specific) |
| Klarna (BNPL) | Stores selling to Gen Z / EU/US | Buy Now, Pay Later options | ~2.9% + 30¢ + Klarna fees |
| Afterpay (Shopify) | Fashion, lifestyle, impulse buys | Interest-free installments | ~4–6% per transaction |
| 2Checkout (Verifone) | International sellers | Works in 200+ countries, flexible | 3.5% + 35¢ |
| Spiltit / Sezzle | Subscription or recurring payments | Alternative BNPL options | 3–6% |
| Shopify + Apple/Google Pay | Mobile-first shoppers | 1-click checkout | Included with Shopify Payments |
Shopify Credit Card & Alternative Payment Options
Beyond gateways, Shopify also supports:
- Credit & Debit Cards (Visa, Mastercard, Amex, Discover)
- Digital Wallets (Apple Pay, Google Pay, Amazon Pay)
- Bank Transfers (varies by country)
- Shopify Merchant Account integrations
The Hidden Costs: Shopify Fees and Chargebacks
Here’s something many new sellers overlook.
If you don’t use Shopify Payments, you’ll pay an extra fee of 0.5%–2% on every sale just for using a third-party gateway.
For example, if you sell $10,000 through Stripe, you’ll pay both Stripe’s fee (around 2.9%) and Shopify’s additional third-party fee.
That difference adds up quickly.
On top of that, every payment provider has its own approach to chargebacks.
Dropshippers, in particular, should be prepared. Shopify Payments and Stripe both provide fraud analysis, but they can freeze accounts if disputes rise too high.
PayPal is notorious for siding with buyers. 2Checkout is more lenient, but charges slightly more. Smart merchants set aside a small contingency fund to cover disputes and refunds.
Read Also: How Much Does it Cost to Start Dropshipping On Shopify in 2025?
Handling Shopify Chargebacks
Chargebacks are part of e-commerce. Here’s what to expect:
- Shopify Payments → Has built-in fraud analysis but may hold funds if chargeback rates are high.
- Stripe → Strong fraud tools, but bans high-risk merchants quickly.
- PayPal → Buyer-friendly, but often sides with customers.
- 2Checkout → More flexible but with higher fees.
Always keep a contingency fund (10% of sales) to cover disputes and refunds.
The Best Shopify Payment Gateway Strategy in 2025
So, what’s the winning approach? For most global sellers, the best strategy isn’t choosing just one gateway.
Instead, it’s about layering them to maximize trust and coverage. Ideally, you’d start with Shopify Payments if it’s available, add PayPal to boost conversions, and include a BNPL option like Klarna or Afterpay if you’re in the fashion or lifestyle space.
If Shopify Payments isn’t available in your country, Stripe or 2Checkout will likely be your best alternative.
By combining these providers, you cover credit cards, PayPal, digital wallets, and installment payments, giving customers every reason to buy without hesitation.
Final Thoughts: Best Shopify Payment Gateways in 2025
At the end of the day, the best payment provider for Shopify is the one that balances low fees, customer trust, and accessibility in your region.
Shopify Payments may be the cheapest and simplest, but PayPal adds credibility, Stripe adds flexibility, Klarna and Afterpay boost sales through installments, and 2Checkout ensures international sellers aren’t left behind.
At One32 Solutions, we’ve helped merchants across the UAE, KSA, and USA set up their stores with the right Shopify merchant services while cutting down on hidden fees and avoiding the pitfalls of chargebacks.
Whether you want a done-for-you solution, we’ll make sure your checkout process is ready to convert. If you want to set it up yourself, get a free consultation.
FAQs:
What payment method should I use for my Shopify store?
The best Shopify Payment Gateways for your store depends on your location, target audience, and business model, but most merchants start with Shopify Payments because it’s easy to set up, has competitive fees, and allows you to accept credit cards, Apple Pay, and Google Pay without third-party integrations.
Which is better, Shopify Payments or Stripe?
Choosing between Shopify Payments and Stripe depends on several factors, your country, volume of sales, business model (subscriptions, digital or physical products, etc.), and how much you value simplicity vs. flexibility. Below is a comparison to help you decide which is better for you.
What is the most used payment method on Shopify?
The most widely used payment method on Shopify is Shopify Payments, Shopify’s built-in payment gateway. It’s popular because it allows merchants to accept all major credit cards, Apple Pay, Google Pay, and local payment options directly through Shopify, without needing a third-party integration.
For global stores, PayPal is also one of the most commonly used payment methods on Shopify because of its huge customer base and trust factor. Many merchants use Shopify Payments as the primary gateway and keep PayPal as a secondary option to maximize conversions.
Which online payment method has the lowest fees?
The payment method with the lowest fees depends heavily on your country, the payment gateway, your Shopify plan, and whether the transactions are domestic or international. However, from the major gateways most Shopify stores use, Shopify Payments usually ends up with the lowest effective fees if it’s available where you are. Here’s why, plus when other options might beat it.
Does Shopify work with Stripe?
Yes, but with a catch. Shopify Payments (Shopify’s built-in payment gateway) is actually powered by Stripe behind the scenes. This means you already get the benefits of Stripe’s infrastructure (like fast processing, high security, and reliable payouts) when you use Shopify Payments.
However, you generally cannot connect Stripe as a separate gateway on Shopify if Shopify Payments is available in your country. Shopify wants you to use Shopify Payments because it’s fully integrated and removes the extra 0.5%–2% transaction fees that Shopify charges for using third-party payment gateways.
If Shopify Payments is not available in your country, you can sometimes use Stripe directly as a third-party payment provider, but you’ll still pay Shopify’s extra transaction fees.
