Taking payments on Shopify in South Africa: PayFast, Yoco, Paystack and Shopify Payments compared.

Picking a payment provider is one of the first decisions on a South African Shopify shop, and one of the most expensive to get wrong. The fees come off every sale, and the payment methods you offer decide whether some customers buy at all.

This guide explains how payments work on Shopify in South Africa, compares the main providers, and shows you how to check the fees yourself. Fees change, so every number below links to its source and was checked at the time of writing (October 2026).

The short answer

• Shopify's own payment service, Shopify Payments, is not available to South African businesses at the time of writing.
• So you connect a third-party provider. PayFast, Yoco and Paystack are three common choices, and each has an app in the Shopify App Store.
• Because you use a third-party provider, Shopify adds its own fee on each sale, on top of the provider's fee.
• The cheapest provider on paper is not always the best. The payment methods your customers want matter as much.

Does Shopify work in South Africa?

Yes. South African businesses can open a Shopify shop, sell to customers here and abroad, and run it day to day like anywhere else. Shopify bills its plans in US dollars, so the monthly cost moves with the exchange rate.

The one real difference is payments. Shopify's own payment service is not available here, so you connect a local provider instead. The rest of this guide explains what that means and what it costs.

Is Shopify Payments available in South Africa?

No. Shopify publishes the list of countries where Shopify Payments is available, and at the time of writing South Africa is not on it. Shopify's help centre says that if your country is not listed, you need to use a third-party payment provider.

This matters for two reasons. First, the extra Shopify fee below. Second, some Shopify features work fully only with Shopify Payments. For example, Shopify's multi-currency help page says only stores using Shopify Payments can use all of its selling-in-several-currencies features. If you plan to sell abroad, read the section on international customers below.

If your business is registered in a country where Shopify Payments is available, the picture is different. This guide is for businesses registered in South Africa.

How the fees stack up

On a South African shop you usually pay two fees per sale:

1. The provider's fee, charged by PayFast, Yoco, Paystack or whoever processes the card or EFT payment.
2. Shopify's third-party transaction fee, a percentage Shopify charges when you use a provider other than Shopify Payments.

At the time of writing, Shopify's South African pricing page lists the third-party fee as 2% on the Basic plan, 1% on Grow, 0.6% on Advanced and 0.2% on Plus. A higher plan costs more each month but takes less from each sale. Once your monthly sales are large enough, the higher plan can work out cheaper overall. Work it out with your own numbers.

Some providers also charge for payouts to your bank, refunds or chargebacks. Look for these on each provider's fee page, not just the headline rate.

PayFast

PayFast, now part of Network International, is one of the longest-running South African gateways. It connects to Shopify through an app in the Shopify App Store, set up with your PayFast merchant ID and key.

Its Shopify page lists card payments, Instant EFT, Mobicred, Apple Pay and Samsung Pay among its methods. That range is its main strength: customers who do not want to use a card still have options.

At the time of writing, PayFast's fees page lists 3.2% plus R2.00 per card payment and 2.0% (minimum R2.00) per Instant EFT payment, before VAT, with no monthly fee. A standard payout to your bank is listed at R8.70 before VAT. Businesses with higher monthly sales can ask for custom pricing.

Good fit for: shops whose customers like to pay by EFT, or who want the widest choice of local payment methods.

Yoco

Yoco is best known for its card machines, and many businesses already use it in person. Its Shopify app connects your Yoco account to your shop without API keys.

The app listing says it accepts Visa, Mastercard and American Express, with Apple Pay and Google Pay. At the time of writing, the listing gives the transaction fee as a maximum of 2.95%, before VAT, for domestic transactions, with lower rates as you sell more. Yoco's Shopify page says payouts happen in two business days with no extra fees. Your exact rate depends on your Yoco plan, and Yoco shows it in the Money section of the Yoco app.

Good fit for: businesses that already use Yoco in store and want online and in-person sales in one place, and whose customers mainly pay by card.

Paystack

Paystack is owned by Stripe and works across several African countries. Its Shopify app lists South Africa among the countries it serves.

We could not confirm Paystack's South African fees from its own site at the time of writing, so we do not quote them here. To check them, open Paystack's South African pricing page and look for three numbers: the fee for local cards, the fee for international cards, and the fee for any EFT or bank payment methods. Then check whether there is a payout fee.

Good fit for: businesses that sell to customers in other African countries as well as South Africa, or that want a provider with a well documented API for custom work.

Other providers worth a look

PayFast, Yoco and Paystack are not the only choices. Ozow focuses on instant EFT, and Peach Payments is another South African gateway. Search the Shopify App Store for providers that support South Africa, and compare them with the same questions below.

Customers abroad

If you sell to people outside South Africa, check three things with each provider before you choose:

1. Does it accept foreign cards? Most do, but some charge more for them.
2. Which currency does the customer pay in? Many South African providers charge in rand. The customer's bank then converts it, and may add its own fee.
3. How does it fit with Shopify Markets? Without Shopify Payments, showing prices in a visitor's currency and charging in that currency are not the same thing. Test a checkout from abroad before you launch.

How to choose

Answer these questions for your own shop:

• How do your customers want to pay? If many prefer EFT, you need a provider that offers it.
• What is your average order value? A flat fee per payment, such as R2.00, matters more on a R100 order than a R2,000 one.
• How many orders a month? Multiply each provider's fee by your real order sizes, not by one example.
• Do you also sell in person? One provider for both can make reconciliation easier.
• Do you sell abroad? See the section above.
• How fast do you need your money? Compare payout times and payout fees.

You can also offer more than one provider. Some shops use one for cards and another for EFT, so customers see every method they expect.

How to check the fees yourself

Fees change and differ by plan, so check them before you sign up:

1. Open each provider's own fee page, not a comparison article.
2. Note the card fee, the EFT fee, any fixed amount per payment, and whether the numbers include VAT.
3. Note payout, refund and chargeback fees.
4. Open Shopify's pricing page for South Africa and note the third-party fee for the plan you want.
5. Add them together for three real orders from your shop: a small one, a typical one and a large one.

Test before you launch

Whichever provider you choose, switch on its test mode in Shopify and place test orders. Then place one real order with a real card, refund it, and check that the money and the refund show up correctly in both Shopify and the provider's dashboard. Do the same for EFT if you offer it.

If you would like help choosing, we set up the provider that fits your customers, connect it to your shop and test every payment method before you go live. Our Shopify service covers the whole build, and a Shopify shop launch has a fixed price on our pricing page.