Commerce guide
Accepting online payments in South Africa
Card, instant EFT and QR, what each costs, and why your checkout conversion depends on offering the method your customer already trusts.
Online checkout in South Africa is not just about cards. Instant EFT carries a meaningful share of local ecommerce, and the method you leave out is the sale you quietly lose.
The methods that matter locally
Cards are the baseline. Beyond that, instant EFT, where the customer pays directly from their bank account and the merchant gets immediate confirmation, carries a real share of South African online payments and is preferred by customers who will not put a card number into a website.
QR payment is the third method, and it works better than you would expect for invoicing and for service businesses because the customer is already familiar with the app.
What online payment costs
Online card rates are higher than in person rates because the risk is higher. iKhokha charges 2.85 percent excluding VAT for online local cards against 2.75 percent in person, and 2 percent for instant EFT, which is notably cheaper than card.
That difference is worth designing for. If instant EFT costs you a percentage point less than a card and your customers are willing to use it, offering it prominently is a direct margin improvement rather than a convenience feature.
Gateway or platform
If you are running a Shopify store, payment is largely handled for you and the decision is which provider to connect. If you are taking payment from your own website or from invoices, you are choosing a gateway and thinking about how it integrates with your accounting.
The integration matters more than it sounds. A payment that arrives in your bank account as a lump settlement of forty transactions, with fees netted off, is a reconciliation problem every single day unless something automates it.
Settlement, refunds and chargebacks
Ask three questions of any provider. When does money actually reach my account. What happens when I need to refund a customer, and does the fee come back. And what is the process when a cardholder disputes a transaction.
Chargebacks are rare and expensive when they happen. Knowing the process in advance, and knowing what evidence you need to keep, is the difference between a resolved dispute and an unexplained deduction.
Do not make the customer work
The most common cause of an abandoned checkout is friction rather than price. Forced account creation, too many fields, and a payment method the customer does not trust all cost more than a tenth of a percentage point on your rate ever will.
Offer the methods your customers already use, keep the form short, and show the total including delivery and VAT before you ask for payment details.
Reconciliation is the hidden running cost
Online payment providers settle in batches with fees netted off, so forty orders arrive as one deposit that matches no single invoice. Somebody has to break that down every day or the bank account stops reconciling.
Ask whether the provider integrates with your accounting package and what it posts. A provider that writes the settlement, the fee and the individual sales correctly saves more time than a small rate difference will ever save you money.
Common questions
01What does it cost to accept online payments in South Africa?
Online local card rates run around 2.85 percent excluding VAT for a small merchant, with instant EFT cheaper at around 2 percent. Rates fall with monthly turnover on most providers.
02Is instant EFT worth offering?
In South Africa, generally yes. It costs less than card on most providers and a meaningful group of customers prefer it to entering card details, so leaving it out costs you sales as well as margin.
03How quickly do online payments settle?
It varies by provider and by your bank, from same day to a few business days. Ask specifically, because settlement timing affects your working capital more than a small rate difference does.
Editorial note
This guide is general buying guidance and not accounting, legal or tax advice. Amounts and deadlines set by SARS change, so confirm the current figures for your own business before you rely on them.