The three main online payment gateways for South African small businesses are Paystack, Yoco, and PayFast. For invoice payments, Paystack offers the best developer integration and card acceptance. Yoco suits businesses already using Yoco card machines for in-person sales. PayFast is the most established SA gateway with broad payment method support including instant EFT. Rebill integrates with all three.
Overview
| Gateway | Card payments | EFT | Setup | Transaction fee |
|---|---|---|---|---|
| Paystack | Yes (Visa, Mastercard, Amex) | Yes (instant EFT) | API/dashboard | ~2.9% + R1.00 |
| Yoco | Yes (Visa, Mastercard) | No (card only) | App/dashboard | 2.95% |
| PayFast | Yes (Visa, Mastercard) | Yes (Ozow/EFT) | Dashboard | 2.0% to 3.5% |
Fees as of early 2026. Check each provider’s website for current rates.
Paystack
Paystack was founded in Nigeria in 2015 and launched in South Africa in 2020. It was acquired by Stripe in 2020, which gives it strong technical infrastructure and ongoing investment.
What Paystack supports:
- Visa and Mastercard (credit and debit)
- American Express
- South African instant EFT via Peach Payments integration
- Recurring billing and subscriptions
- Payment links (shareable URLs)
Fees:
- 2.9% + R1.00 per successful transaction
- No monthly fee
- No setup fee
Best for: Businesses that want a robust, developer-friendly payment gateway. Paystack has a well-documented API and strong uptime. It works well for invoice payments because clients can pay by card without having a Paystack account.
Limitations: Paystack requires business verification (takes 1 to 3 business days). No in-person card machine is available in South Africa. It does not natively support direct EFT (clients must use the instant EFT option).
Yoco
Yoco is a Cape Town-based payments company known for its card machines used in cafes, markets, and small retail shops. It also offers an online payment solution for invoices and e-commerce.
What Yoco supports:
- Visa and Mastercard (credit and debit)
- Payment links via the Yoco dashboard
- Online checkout
Fees:
- Online transactions: 2.95% per transaction
- No monthly fee for the basic plan
- Yoco card machines range from R999 to R2,499 (one-time purchase)
Best for: Businesses that want a single provider for both in-person and online payments. If you already use a Yoco card machine at your market stall, shop, or studio, adding Yoco to your Rebill invoices gives you one payment dashboard for everything.
Limitations: Yoco does not support EFT payments. Clients must pay by card. American Express is not supported. No recurring billing API (recurring billing must be done manually).
PayFast
PayFast is the most established South African payment gateway, founded in 2007. It is widely used across South African e-commerce and supports the broadest range of payment methods.
What PayFast supports:
- Visa and Mastercard (credit and debit)
- Instant EFT via Ozow
- SCode (EFT at ATM)
- Masterpass
- Discovery Miles
- Recurring billing subscriptions
Fees:
- Credit/debit cards: 2.0% to 3.5% (tiered by volume)
- Instant EFT: 1.5% to 2.0%
- No monthly fee for the basic plan
Best for: Businesses that want the widest payment method coverage. PayFast’s instant EFT option (via Ozow) lets clients pay by bank transfer in real time, which some South African clients prefer over entering card details. If your clients are wary of paying by card, PayFast’s EFT option removes that barrier.
Limitations: PayFast’s dashboard is older than Paystack’s. Verification and setup can take longer. The tiered fee structure is more complex.
Quick answer
What is the best payment gateway for small businesses in South Africa?
For South African small businesses using invoicing software, the best payment gateway depends on your needs. Paystack is the strongest choice for online invoice payments: it supports Visa, Mastercard, and Amex, has competitive fees (2.9% + R1), and integrates cleanly with invoicing tools like Rebill. PayFast is the best option if your clients prefer EFT, as it supports instant EFT via Ozow in addition to cards, and has a lower card rate (from 2%) at higher volumes. Yoco is ideal if you already use Yoco card machines for in-person sales and want a single provider. All three are reliable, South African businesses, and support ZAR transactions. Rebill integrates with all three so you can use whichever gateway you already have or prefer, or connect multiple gateways and let clients choose.
Which gateway should you use?
Choose Paystack if:
- You want the best overall developer and API experience
- You send invoices to clients who pay by credit or debit card
- You want a payment link that looks professional and loads fast
Choose Yoco if:
- You already have a Yoco card machine for in-person sales
- You want one dashboard for all your payments
- Your clients pay by Visa or Mastercard (you do not need EFT)
Choose PayFast if:
- Your clients prefer EFT over card payments
- You need the widest range of payment methods
- Your transaction volume is high enough to benefit from PayFast’s tiered rates
Use all three with Rebill: Rebill lets you connect Paystack, Yoco, and PayFast simultaneously. You can set a default gateway per invoice or give clients the choice. This is particularly useful if some clients prefer card payments and others prefer EFT.
What about transaction fees?
On a R5,000 invoice, here is what each gateway charges (approximate):
| Gateway | Method | Fee on R5,000 |
|---|---|---|
| Paystack | Card | R146.00 (2.9% + R1) |
| Yoco | Card | R147.50 (2.95%) |
| PayFast (high volume) | Card | R100.00 (2%) |
| PayFast | Instant EFT | R75.00 to R100.00 |
For most small businesses, the difference between Paystack and Yoco is negligible. If transaction volume is significant, PayFast’s tiered rates become more competitive.
Frequently asked questions
Can I use Paystack, Yoco, and PayFast together?
Yes, if you use invoicing software like Rebill. Rebill lets you connect all three gateways to your account and assign a default gateway per invoice. You can also present clients with multiple payment options. This is useful if you have clients who prefer different payment methods.
Which payment gateway has the lowest fees in South Africa?
PayFast has the lowest card rates at higher transaction volumes, starting from 2% for businesses processing over a certain monthly threshold. For lower volumes, all three gateways charge between 2.9% and 3.5% per transaction. Instant EFT via PayFast (through Ozow) can be cheaper than card payments at around 1.5% to 2%.
Do clients need to have a Paystack or Yoco account to pay?
No. Clients pay using a standard payment form that accepts their card details directly. They do not need to register or create an account with any payment provider. The payment link opens a secure page where they enter their card number, expiry date, and CVV, and the payment processes immediately.
How long does it take for funds to arrive after a Paystack/Yoco/PayFast payment?
Settlement times vary by gateway. Paystack typically settles within 1 to 2 business days. Yoco settles within 1 to 3 business days. PayFast settles within 1 to 2 business days for card payments, and same-day for instant EFT in some cases. All three automatically transfer funds to your South African bank account on their settlement schedule.