Choosing the right payment gateway for your Shopify store can save you thousands in fees and directly impact your conversion rate. We break down the top options — Shopify Payments, Stripe, PayPal, and Square — with real fee comparisons and honest recommendations for different store sizes and sales channels.
Every Shopify store needs a payment gateway — the thing that actually moves money from your customer's card to your bank account. Pick the wrong one and you're paying unnecessary fees, hurting conversion rates, or locking yourself out of features you need. Pick the right one and it just works.
Here's the honest breakdown of the best payment processors for Shopify stores right now.
Shopify Payments is the payment gateway built directly into Shopify. When you use it, you avoid the additional 0.5%–2% fee Shopify charges on third-party gateways. It's automatically set up with your store — no extra accounts, no API keys to paste, no separate monthly fees.1
Best for: most Shopify stores, especially new sellers and anyone who wants the simplest possible setup.
Trade-off: you're locked into Shopify's rate card. If you process high volume, you might negotiate better rates elsewhere — but you'd lose the native fee waiver.
Stripe powers Shopify Payments behind the scenes, but you can also use it directly as a third-party gateway. It offers deeper customization: saved payment methods, subscription billing, and a richer API for custom checkout flows.
Best for: stores with recurring billing, custom checkout experiences, or high-volume merchants who need advanced fraud tools.
Trade-off: you'll pay Shopify's third-party transaction fee (typically 0.5%–2% extra on top of Stripe's processing rates) unless you're on Shopify Payments.
PayPal is the most recognized digital wallet globally. For many small businesses, offering PayPal at checkout is table stakes — customers who don't want to enter card details can pay with one click. It's quick to set up and doesn't require a merchant account.
Best for: small businesses, international stores, and any store where buyer trust is a concern.
Trade-off: PayPal's rates are generally higher than Stripe or Shopify Payments, and you'll still pay Shopify's third-party fee on top. It's best as a secondary option, not your primary gateway.
Square is the go-to for merchants who sell both online (Shopify) and in person (at markets, pop-ups, or a physical store). Square's POS hardware syncs with your Shopify inventory, giving you a single view of stock across channels.
Best for: omnichannel sellers, brick-and-mortar businesses adding an online store, or anyone who already uses Square for in-person payments.
Trade-off: Square's online rates are competitive but not the lowest. Like PayPal, it's a third-party gateway on Shopify, so the extra fee applies.
| Gateway | Transaction Fees (Online) | Setup Ease | Best For |
|---|---|---|---|
| Shopify Payments | 2.4%–2.9% + 30¢ (varies by plan) | Instant — built in | Most Shopify stores |
| Stripe | 2.9% + 30¢ + Shopify's third-party fee | Moderate — API setup | Power users, subscriptions |
| PayPal | 2.99% + 49¢ + Shopify's third-party fee | Easy — plug and play | Small biz, buyer trust |
| Square | 2.9% + 30¢ + Shopify's third-party fee | Easy — account sync | Omnichannel sellers |
By volume: If you're doing under $50k/year, Shopify Payments is almost certainly your best bet. Above that, it's worth running the math on Stripe's negotiated rates minus the third-party fee.
By location: Shopify Payments supports 23+ countries. If your primary market isn't covered, Stripe has broader international support and handles 135+ currencies.
By sales channel: Selling in person too? Square's inventory sync is genuinely useful. Selling mostly online? Shopify Payments or Stripe will serve you better.
For 80% of Shopify stores, Shopify Payments is the right answer — it's free (no extra gateway fee), pre-installed, and good enough. Add PayPal as a secondary option for customer comfort. Only reach for Stripe or Square if you have a specific need they solve better.
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