Shopify Payment Gateways: Complete Guide to Payment Processing

Shopify Payments & eCommerce Payments: Key Takeaways

Payment processing is a strategic growth lever, not just a technical requirement. On Shopify, how you configure payments directly affects margins, conversion rates, customer trust, and your ability to sell internationally.

Why Start With Shopify Payments

• Lower total fees: No extra Shopify transaction fees (0.5–2%) that apply to third‑party gateways.
• Competitive card rates (online):
• Basic: 2.9% + $0.30
• Shopify: 2.6% + $0.30
• Advanced: 2.4% + $0.30
• Plus: typically ~2.15% + $0.30 (negotiated)
• Unified admin: Payouts, disputes, and reports managed in Shopify.
• Shop Pay: High‑converting accelerated checkout, plus Shop Pay Installments (BNPL) in the US.
• Multi‑currency: Built‑in support when combined with Shopify Markets.

Setup is done in Settings → Payments → Activate Shopify Payments, where you add business details, bank info, verify identity, and choose payout schedule. Activation usually takes 10–15 minutes.

If Shopify Payments isn’t available in your country or your industry is restricted, you’ll need a third‑party gateway.

Understanding Fees & When to Upgrade Plans

If you use third‑party gateways, Shopify adds an extra fee on top of the gateway’s own rate:

• Basic: +2.0%
• Shopify: +1.0%
• Advanced: +0.5%

Example: Gateway at 2.9% + $0.30 on Basic → 4.9% + $0.30 effective.

Because of this, most eligible merchants should use Shopify Payments as their primary processor.

Plan upgrade break‑evens (approx.):

• Basic → Shopify: consider upgrading when monthly revenue > ~$7,500
• Shopify → Advanced: consider upgrading when monthly revenue > ~$40,000

Run the math for your own AOV, volume, and mix of payment methods to confirm.

Alternative Gateways & When to Use Them

Summary of Key Takeaways

• Best default gateway: Use Shopify Payments as your primary gateway whenever it’s available; pair it with PayPal as a secondary option for buyer trust and preference.
• Fees comparison: Shopify Payments typically costs 2.4–2.9% + $0.30 per transaction (depending on plan) with no extra Shopify transaction fee. Third‑party gateways like Stripe or PayPal incur similar base rates plus an extra 0.5–2% Shopify surcharge unless Shopify Payments is also active.
• Setup steps for Shopify Payments: Go to Settings → Payments → Activate Shopify Payments, then complete business verification (legal entity, tax ID, bank account, identity documents). Approval usually takes 1–3 business days and requires being in a supported country and complying with Shopify’s terms.
• Multiple gateways: You can run one primary credit card processor (Shopify Payments or a third‑party like Stripe) plus multiple alternative methods (PayPal, Apple Pay, Google Pay, Klarna, Affirm, Afterpay, etc.). You cannot run Shopify Payments and another credit‑card gateway in parallel as co‑primary processors.
• International payments: Use Shopify Payments + Shopify Markets to sell in 130+ currencies, show localized prices, and enable local payment methods (e.g., iDEAL, Bancontact). In regions where Shopify Payments isn’t available, configure regional third‑party gateways while still using Shopify Payments where it is supported.
• Buy-now-pay-later (BNPL): Enabling Shop Pay Installments, Klarna, Affirm, or Afterpay can lift AOV by ~20–50% and conversion by ~10–30%, especially when AOV is >$50 (fashion, electronics, furniture, etc.). Expect 3–6% per‑transaction fees, which are often offset by higher revenue.

Expert Resources

• Shopify Payments: Official setup, supported countries, fees, and payouts: help.shopify.com/en/manual
• Stripe (for Shopify where applicable): Payment Intents, methods, PCI, and integration patterns: docs.stripe.com/payments
• PayPal: Checkout, subscriptions, buyer protection, and merchant tools: developer.paypal.com/docs/
• Apple Pay for merchants: Requirements, UX guidelines, and processing: developer.apple.com/apple-pay/
• Klarna for merchants: BNPL integration, onboarding, and settlement: docs.klarna.com
• Shopify Payments Apps API: Architecture for third‑party payment integrations: shopify.dev/docs/apps

Summary of Shopify Payment Gateway Guidance

• Best primary gateway: Shopify Payments (when available in your country).
• No extra 0.5–2% Shopify surcharge that applies to third‑party gateways.
• Built‑in fraud analysis and access to Shop Pay accelerated checkout.
• Typical fees: 2.4–2.9% + $0.30 per transaction, with lower rates on higher plans.
• If Shopify Payments is not supported in your country, Stripe is generally the best alternative.
• Fee comparison:
• Shopify Payments: ~2.4–2.9% + $0.30.
• Third‑party gateways (e.g., Stripe, PayPal): their own fee plus Shopify’s extra 0.5–2%.
• Using PayPal as the main gateway can reach ~5–6% total per transaction vs 2.4–2.9% with Shopify Payments.
• Setting up Shopify Payments:

1. In Shopify admin, go to Settings → Payments.
2. Click “Activate Shopify Payments.”
3. Enter required business details (e.g., EIN, bank account, SSN in the US).
4. Complete identity verification.
5. Payouts typically start within 2–3 business days.

• Your business must be in a supported country and sell permitted products.
• Using multiple gateways:
• You can have one primary gateway plus alternative methods.
• Common setup:
• Primary: Shopify Payments.
• Alternatives: PayPal Express, Apple Pay, Google Pay, Shop Pay.
• Offering 3–4 payment options can increase conversion by ~10–15%.
• International payments:
• Shopify Payments supports 130+ currencies.
• Shoppers see prices in their local currency and can pay with local methods.
• You receive payouts in your base currency with about 1.5% currency conversion fee.
• In regions without Shopify Payments, use Shopify Markets to configure region‑specific gateways.
• Shop Pay benefits:
• Accelerated checkout that stores customer info for one‑tap purchases across Shopify stores.
• Can improve conversion by 1.72× vs standard checkout and is 4× faster than regular checkout.
• Free to enable for stores using Shopify Payments; there’s effectively no downside to turning it on.

Official Resources

• Shopify Payments: shopify.com/payments
• Stripe Docs: stripe.com/docs
• PayPal Developer: developer.paypal.com
• Apple Pay for Merchants: developer.apple.com/apple-pay/
• Klarna for Business: klarna.com/business/