Shopify Payments vs Stripe vs PayPal: 2026 Fee Comparison

Your Shopify dashboard shows fees as one number. It does not tell you that PayPal orders cost you 2.8 cents more per dollar than Shopify Payments orders on the same plan — because Shopify mixes every gateway into a single fee line.

This comparison breaks down the real 2026 per-sale cost of the three most common Shopify gateways, explains the surcharge trap that makes third-party gateways quietly expensive, and shows how to see your actual per-gateway cost from your Orders CSV.

The 30-second answer

On a $100 sale, Shopify Basic plan, US domestic online transaction:

Rates verified against Shopify's 2026 pricing page and published gateway fees. International and card-present rates differ.

Same processing economics for Stripe and Shopify Payments (both ~2.9% + $0.30) — the entire $2 gap is the Shopify third-party surcharge. That surcharge is the single biggest lever in Shopify gateway cost.

The surcharge trap most merchants miss

Shopify charges two separate fees when you use a third-party gateway (Stripe, PayPal, Authorize.net):

1. The gateway's processing fee — what Stripe or PayPal charges to move the money (2.9% + $0.30 for Stripe, ~3.49% + $0.49 for PayPal).
2. Shopify's third-party transaction surcharge — an extra 2% (Basic), 1% (Grow), or 0.5% (Advanced) that Shopify adds because you are not using Shopify Payments.

The dashboard rolls both into one "transaction fees" line, so most merchants see a single ~5% number and assume that is just "the cost of accepting cards." It is not — half of it is avoidable by using Shopify Payments, or reducible by upgrading plans (the surcharge drops to 0.5% on Advanced).

Why use Stripe or PayPal at all, then?

If Shopify Payments is cheapest, why do stores add the others?

• Payment methods Shopify Payments lacks — PayPal Wallet, some regional methods, Buy Now Pay Later options.
• Buyer trust / conversion — some customers only check out if they see the PayPal button. The conversion lift can outweigh the fee.
• International coverage — certain countries or card types process more reliably through Stripe.

The smart pattern most stores land on: keep Shopify Payments as the default, add PayPal as an express option. You pay the surcharge only on the PayPal orders (where the conversion benefit justifies it), and Shopify Payments handles the majority at the lower rate.

The hidden cost: refunds still keep the fee

None of the three gateways refund their processing fee when you refund a customer. So a refunded $100 order costs you $3.20 (Shopify Payments) or $5.98 (PayPal) — with zero revenue. Higher-fee gateways make refunds more expensive. If your refund rate is high on PayPal orders specifically, the cost compounds. See the full refund-fee breakdown →

See your real per-gateway cost

The dashboard will not break out per-gateway cost for you. To see it:

1. Export your Shopify Orders CSV (Admin → Orders → Export → All orders, Plain CSV).
2. Drop it into the free CSV Profit Checker.
3. It groups orders by PaymentMethod, applies the right rate per gateway, and shows each gateway's effective fee % and total — next to refunds, shipping, and COGS.

You will usually find one gateway with a much higher effective rate than you expected — often PayPal, because the surcharge + higher base rate stack. That is the gateway to nudge customers away from (or negotiate down).

When upgrading the Shopify plan beats switching gateways

If you are on Basic and using third-party gateways heavily, the 2% surcharge may cost more than upgrading to Grow ($105/mo, 1% surcharge) or Advanced ($399/mo, 0.5% surcharge). Break-even: if your monthly sales through third-party gateways exceed ~$10,500, Grow's lower surcharge pays for the plan difference. Run the numbers on your real CSV rather than guessing.