Which payment gateway should a South African online store use?

For most small South African stores, the lowest published debit-card rate right now is Bob Pay's 1.95%, with no monthly fee, and the cheapest way to get paid is still a bank payment such as instant EFT or Capitec Pay, at about 1.5%. Payfast costs more per card sale but is the name many local shoppers already know. The bigger mistake is ignoring what your store platform adds on top: Shopify charges up to 2% more per sale when you use a local gateway, which can cost more than the gateway itself.

Below are the published fees for each provider, worked out on a R1 000 order, and then the platform line. If you'd rather skip to what we use, our online stores run on Sirat Retail OS, which takes 0% of your sales.

What does a payment gateway actually do?

A payment gateway is the service that takes the customer's card or bank payment on your checkout page, checks it with the bank and pays the money into your account, minus its fee. You don't need a separate merchant account from your bank for most of the providers below. They hold the money briefly and pay it out to you.

Every gateway charges per successful payment. Some add a fixed amount per sale, some charge to pay out to your bank, and a few charge a monthly fee. Those small extras matter more than the headline percentage when your average order is small.

What does each gateway charge on a R1 000 sale?

These are each provider's own published rates for a new, small merchant, checked September 2026, excluding VAT as the providers quote them. Higher-volume stores get lower rates from most of them.

Provider	Card payment	Bank payment (EFT, Capitec Pay)	Pay later option	Monthly fee
Payfast	3.2% + R2 = R34.00	2.0%, min R2 = R20.00	Payflex: 5.45% + R5 = R59.50	None
Yoco online	2.95% = R29.50	Not published	Not published	None
Ozow	2.85%, min R1 = R28.50	1.5%, min R1 = R15.00	4.99% + R4 = R53.90	None
Peach Payments (Growth)	2.95% + R1.50 = R31.00	1.5% + R1.50 = R16.50	Payflex: 5.25% + R4 + R1.50 = R58.00	None
Bob Pay	Debit 1.95% = R19.50, credit 2.70% = R27.00	1.5%, max R15 = R15.00	Not listed	None

A few things the table can't show:

• Yoco publishes 2.95% for local online payments on its gateway page, and a range of 2.55% to 2.95% on its online payments page, with custom rates above R200 000 a month. We used the top of the range.
• Bob Pay charges less on debit cards than on credit cards. Most comparisons quote one card rate, so check how your customers pay. Bob Pay's rates drop again once you process more than R500 000 a month.
• Ozow started as an instant EFT provider and now takes cards too. Its bank-payment rate of 1.5% covers Capitec Pay, Absa Pay, Nedbank Direct EFT and PayShap.
• Peach Payments adds R200 a month if you want to save customers' cards for repeat billing, and its Enterprise plan carries a R300 monthly account fee.

What does it cost to get the money out?

Payout fees are charged when the gateway sends your balance to your bank, not per sale.

Provider	Payout fee	Refund fee
Payfast	R8.70 per standard payout; 0.8% (min R14) for an immediate payout	R2
Ozow	R3 per payout	R3
Peach Payments	Free daily settlement	Not listed
Bob Pay	R5 per payout, free above R20 000	R2.50

Yoco's gateway page doesn't list a payout fee. Checked September 2026, on the same provider pages linked above.

If you pay out once a week, these are small numbers. If you want your money daily, Payfast's standard payout alone is about R260 a month.

What about buy now, pay later?

Payflex lets a shopper pay in two, three or four interest-free parts while you get the full amount upfront, according to Payflex's merchant page. Payflex carries the risk if the shopper stops paying. That's why it costs roughly double a card payment: about R58 to R60 on a R1 000 order through Payfast or Peach.

Payflex doesn't publish its direct merchant rate. It says you pay a monthly service fee plus a fee on each successful order, and quotes the numbers when you apply. It's worth offering if your products sell for R500 or more and people hesitate at the full price. On a R150 order it rarely earns its fee.

What does your store platform add on top?

This is the line most gateway comparisons skip.

Shopify's own card processing, Shopify Payments, isn't available in South Africa. So every Shopify store here uses a local gateway, and Shopify adds its own third-party transaction fee on each of those sales: 2% on Basic, 1% on Grow, 0.6% on Advanced. Shopify's help centre says the fee is worked out on the full order total, including delivery. It doesn't apply to manual payments such as a bank deposit you mark as paid yourself.

On a R1 000 card order on Shopify Basic through Payfast:

Line	Amount
Payfast, 3.2% + R2	R34.00
Shopify third-party fee, 2%	R20.00
Total taken from the sale	R54.00

That's 5.4% of every order before you've paid for the plan or any apps. We cover the rest of the bill in what Shopify really costs in South Africa.

WooCommerce takes no cut of sales; you pay the gateway only. Shopify vs WooCommerce in South Africa compares the two in more detail.

Sirat Retail OS also adds 0%. The store owner pays only the payment provider's fee.

Which one should you choose?

Start with how your customers pay, then the fee.

• Most customers pay by debit card or EFT: Bob Pay or Ozow will usually cost least.
• Customers expect to see a familiar name at checkout: Payfast has been around the longest of this group. You pay about R5 to R15 more per R1 000 card order than the cheaper options for that familiarity.
• You already use Yoco card machines in your shop: Yoco's gateway keeps everything on one dashboard. Check whether that's worth 2.95% against the cheaper rates above.
• You sell to other businesses, or larger orders: a bank-payment option at 1.5% saves real money, and Bob Pay caps its EFT fee at R15 no matter how big the order is.
• You sell items above R500 and see abandoned carts: add Payflex.

You don't have to pick only one. Most stores offer a card option and a bank option side by side, and the customer chooses.

What we set up for Retail OS stores

Our online stores take payments through Bob Pay, Paystack, Payfast, Payflex, PayJustNow and EFT. We chose Bob Pay for its low debit-card rate, its low EFT cap and no monthly fee. Connecting payments is part of the once-off store setup, which we quote per store, and Retail OS plans start at R400 a month. Nothing is added to your sales.

This isn't the right fit if you're selling a handful of items a month. At that size a payment link from your gateway, or a small WooCommerce shop, will cost you less. It suits shops that already trade, and that want the website and the till counting the same stock. Victoria Packaging, Sizabantu Fabrics and Cell Trader are among the stores on it.

If you'd like to know what your own fees would be at your order sizes, see how Sirat Retail OS works, get an estimate at /price, or WhatsApp us on +27 73 453 8352.