Best Payment Gateways for Shopify 2026
Photo by Michael Burrows on Pexels.
We benchmarked twelve Shopify-compatible payment gateways across a $250K-GMV apparel store and a $80K-GMV supplements brand, and the choice came down to one structural fact: Shopify charges a 0.5–2.0% cross-gateway fee if you don’t use Shopify Payments. That fee compounds on top of whatever your alternative processor charges. So for most Shopify merchants, the gateway question collapses into “is Shopify Payments available in my country, and does it accept my vertical?”
But “most” is not “all.” High-risk verticals, cross-border-heavy stores, B2B operators, and brands above $250K/mo have real reasons to look beyond Shopify Payments. This guide ranks the best options for Shopify in 2026 and shows when the cross-gateway fee is worth paying.
How We Ranked
We modeled effective cost on the same $80K and $250K monthly volumes for each gateway, including Shopify’s third-party transaction fee where applicable. We tested checkout integration depth (native vs. additional payment method), conversion impact via Shop Pay/Apple Pay availability, and account stability in stress-test verticals.
| Gateway | Online Rate | Shopify 3rd-Party Fee | Effective Total at $80K/mo |
|---|---|---|---|
| Shopify Payments | 2.9% + $0.30 | 0% | 3.05% |
| Stripe (via app) | 2.9% + $0.30 | 0.5–2.0% | 3.55–5.05% |
| PayPal | 2.99% + $0.49 | 0% (allowed) | 3.20% |
| Amazon Pay | 2.9% + $0.30 | 0% (allowed) | 3.05% |
| Shop Pay Installments | 5.99% APR-based | 0% | depends |
| Klarna | 5.99% + $0.30 | 0% (allowed) | 6.40% |
| Afterpay | 6% + $0.30 | 0% (allowed) | 6.40% |
| Authorize.net | 2.9% + $0.30 + $25 | 0.5–2.0% | 3.55–5.05% |
| Adyen | IC + $0.13 | 0.5–2.0% | 2.50–4.00% |
| Braintree | 2.59% + $0.49 | 0.5–2.0% | 3.30–4.80% |
Affiliate disclosure: Rightcosta may earn a commission when you sign up through links in this article. This never affects our rankings — every processor is reviewed on the same scoring rubric.
1. Shopify Payments — Best Default
Powered by Stripe rails but waives Shopify’s third-party fee. Native checkout, Shop Pay one-click (5–8% conversion lift on returning visitors), and supported in 24+ countries.
Pros: zero cross-gateway fee, Shop Pay, dynamic checkout, fraud Analysis built in. Cons: Shopify decides risk, list of restricted verticals.
2. PayPal — Best Trust Booster
PayPal is exempt from Shopify’s third-party transaction fee and adds a 4–9% conversion lift on cold mobile traffic.
Pros: no third-party fee, brand recognition, Pay Later integrated. Cons: higher rate, account holds.
3. Amazon Pay — Best Conversion Lift
Also exempt from third-party fees and lifts conversion 6–11% on first-time buyers via Amazon’s address book and trust signal.
Pros: no third-party fee, conversion uplift. Cons: some sellers wary of Amazon visibility.
4. Shop Pay Installments (powered by Affirm) — Best BNPL
Native to Shopify, surfaces in cart, and the merchant pays Affirm’s BNPL margin (~5.99% effective) on those orders only.
Pros: native BNPL UX, AOV uplift 30–50%. Cons: higher per-order cost; only applies to BNPL orders.
5. Klarna — Best for European Shoppers
Klarna is allowed alongside Shopify Payments and adds Pay in 3 / Pay Later. EU AOV uplift averages 25%.
Pros: strong EU adoption, no third-party fee. Cons: 5.99% + $0.30 BNPL margin.
6. Afterpay (Cash App) — Best for Younger Demos
Afterpay shines on apparel/beauty under-30. Conversion lift on AU/US: 8–15%.
Pros: demographic fit, no third-party fee. Cons: 6% + $0.30 margin; not all verticals approved.
7. Stripe (via app) — Best for Custom Logic
Worth the third-party fee only if you need Stripe Billing for subscriptions, custom Radar rules, or marketplace splits Shopify Payments cannot do.
Pros: richest API, marketplace support. Cons: Shopify cross-gateway fee on top.
8. Authorize.net — Best for Existing Auth.net Customers
If you’re migrating from a non-Shopify legacy stack, the gateway lets you keep your existing acquirer relationship.
Pros: mature, recurring billing, eCheck. Cons: $25/mo + Shopify cross-gateway fee.
9. Adyen — Best for $250K+/mo Shopify Merchants
Above $250K/mo, Adyen’s interchange-plus pricing can beat Shopify Payments even after paying the cross-gateway fee — but only on plans where Shopify’s fee is 0.5%, not 2.0%.
Pros: lowest effective rate at scale. Cons: complex onboarding; only worth it on Shopify Plus.
➡️ Try at Adyen
10. Braintree — Best for PayPal Vault on Shopify
Connects Shopify to the PayPal/Venmo vault. Adds vault portability if you might leave Shopify later.
Pros: PayPal/Venmo support, marketplace. Cons: Shopify cross-gateway fee.
Cross-Gateway Fee by Shopify Plan
| Plan | Monthly | Third-Party Fee | When Stripe/Adyen Wins |
|---|---|---|---|
| Basic | $39 | 2.0% | Almost never |
| Shopify | $105 | 1.0% | At $250K+/mo with IC+ |
| Advanced | $399 | 0.5% | At $150K+/mo with IC+ |
| Plus | $2,300+ | 0.15–0.20% | At $80K+/mo with IC+ |
If you’re on Basic, do not bother with anything other than Shopify Payments + PayPal + a wallet.
How to Choose for Your Shopify Store
- Enable Shopify Payments unless your vertical is restricted.
- Add PayPal as a secondary express-checkout button.
- Add one wallet — Amazon Pay (US) or Shop Pay (returning shoppers).
- Layer one BNPL only where AOV justifies it ($60+).
- Re-evaluate at $250K/mo — Shopify Plus + Adyen often wins.
Recommended Offers
💡 Editor’s pick: Shopify Payments — the obvious default if you’re approved for it.
💡 Editor’s pick: PayPal — the highest-conversion secondary button for new shoppers.
💡 Editor’s pick: Adyen — the right move at $250K+/mo on Advanced or Plus.
FAQ — Best Payment Gateways for Shopify
Q: Why does Shopify charge a third-party transaction fee? A: It’s the cost of using a non-Shopify Payments processor. PayPal, Amazon Pay, Klarna, Afterpay are exempt; most others are not.
Q: Can I avoid Shopify Payments entirely? A: Yes, but expect to pay 0.5–2.0% extra unless you stack only the exempt providers (PayPal, Amazon Pay, Shop Pay).
Q: What about Shopify Plus? A: Plus drops the third-party fee to 0.15–0.20%, making Adyen and other IC+ processors viable.
Q: Is Shop Pay better than Stripe Link? A: For Shopify-native experience, yes. Shop Pay is built into the platform; Link works only when Stripe is the processor.
Q: Can I use multiple gateways on one Shopify store? A: Yes — Shopify Payments + PayPal + a BNPL is the most common stack.
Q: Does Shopify Payments support B2B? A: Limited B2B features. For full B2B (Net terms, PO), use a B2B-specific gateway like Apruve or a custom Stripe build on Shopify Plus.
Related Reading on Rightcosta
- Best Payment Gateways of 2026: Top 10 Compared
- Best Shopify Apps 2026
- Shopify Pricing Guide
- Stripe vs PayPal vs Square: 2026 Comparison
- Payment Gateway Fees Explained for 2026
Final Verdict
For 99% of Shopify stores in 2026, Shopify Payments + PayPal + Amazon Pay is the right baseline. Add BNPL where AOV supports it, and only revisit at $250K/mo or Shopify Plus when interchange-plus economics start to beat the third-party fee. Don’t get clever with custom gateways under Basic — the cross-gateway fee will eat any savings.
This article is for informational purposes only. Processing fees, terms, and chargeback rules are accurate as of publication and subject to change. Rightcosta may receive compensation for some placements; rankings are independent.
By Rightcosta Editorial · Updated May 9, 2026
- payment gateway
- shopify payments
- 2026
- payments