Shopify Payment Providers in 2026: Shopify Payments vs Third-Party Gateways, Fees and Setup

Two ways to take payments on Shopify

• Shopify Payments: Shopify's built-in payment processing, set up in your admin, with cards, wallets such as Apple Pay and Google Pay, Shop Pay and, in many countries, local payment methods. Payouts, disputes and reporting live inside Shopify.
• Third-party payment providers: outside gateways installed as payment apps, such as PayPal, regional providers or payment orchestration platforms. Shopify charges an additional transaction fee on the orders they process.

Shopify's third-party transaction fee

When an order is paid through a provider other than Shopify Payments, Shopify adds its own fee on top of whatever the provider charges:

Card rates differ by country; check the rates for your market in your Shopify admin. One newer detail: since 12 May 2025, for stores created after that date, the third-party fee also applies to the store-credit and gift-card portion of an order, even when the card payment runs on Shopify Payments.

What it costs per order

On a $100 order, with an outside provider charging 2.9% + 30¢:

If you must use an outside provider, a higher plan can pay for itself. On annual billing, Grow costs $50 a month more than Basic but halves Shopify's fee from 2% to 1%, so the two break even at about $5,000 a month in sales through the outside provider. Above that, Grow is cheaper. Run your own numbers with our Shopify plan calculator.

When a third-party provider makes sense

• Shopify Payments isn't available to you because of your country or business type. Turkey is one example: stores there use local providers such as iyzico, PayTR or the Craftgate payment orchestration platform.
• Your customers expect a specific method that your Shopify Payments setup doesn't cover, such as PayPal in many markets or a local wallet.
• You operate at high volume and can negotiate rates low enough to absorb Shopify's fee, often combined with the Plus plan's 0.2% fee.
• You need payment orchestration: routing payments across several acquirers to raise approval rates or keep taking payments during an outage.

Each additional provider can add Shopify's fee to the orders it processes, so add a second gateway only for a clear reason.

Setting up payments in Shopify

Shopify Payments

1. Go to Settings > Payments in your Shopify admin and activate Shopify Payments.
2. Enter your business details, bank account and identity verification. Have these ready before launch; missing verification can delay or hold payouts.
3. Turn on the wallets and local methods you want to offer.
4. Place a real test order and refund it to confirm the full flow.

A third-party provider

1. Open a merchant account with the provider and get your credentials.
2. In Settings > Payments, search for the provider and activate its payment app.
3. Enter your credentials, then test successful payments, failed payments and refunds in test mode.
4. Switch to live mode and confirm with a small real order. Check that orders are marked as paid and that purchases reach GA4 and your ad platforms: thank you page tracking guide.

Common payment problems

• Payouts on hold: sudden sales spikes, missing verification or high dispute rates can trigger holds: Shopify Payments payouts on hold.
• Orders stuck as pending: the provider's callback or notification settings are incomplete.
• Refunds not syncing: start refunds from the Shopify order so both systems update.
• Unexpected fees: check whether an extra gateway or gift-card orders are triggering Shopify's third-party fee.

For the newest local methods added to Shopify Payments, see Shopify Payments' new local payment methods. To see what's left of each sale after all fees, try our Shopify profit calculator.

Sources: CommercePundit, eightx. Rates vary by country and change over time; check your Shopify admin. Information current as of 12 November 2026.