Payment gateway fees comparison South Africa: the standard card rate runs from 2.95% to 3.5% per transaction, but that single number tells you less than half the story. Every South African ecommerce store — whether you're running a Shopify store in South Africa or on another platform — pays a transaction percentage, a flat fee per sale, a payout fee when funds hit your bank account, and potentially a BNPL premium if you offer instalment options.
The gateway with the lowest advertised rate is not always the cheapest gateway for your store. This post covers six major South African payment gateways — PayFast, Peach Payments, Yoco, Ozow, Stitch, and PayGate — with the 2026 published rate schedules, a worked example at R100,000 monthly GMV, and a breakdown of the cost layers that don't appear in the headline figure.
All rates are ex VAT; South African VAT applies to merchant service fees. Rates are sourced from mid-2026 published fee schedules — verify current pricing directly with each provider before signing up, as rates change.
If you use SA ecommerce payment methods beyond cards and EFT — BNPL, digital wallets, or QR payments — the comparison shifts further. We cover those layers in the hidden costs section below.
Quick Answer
A payment gateway fees comparison in South Africa shows card rates ranging from 2.95% (Peach Payments, Yoco, Stitch) to 3.5% (PayGate), with EFT rates as low as 1.5% (Ozow, Peach Payments). PayFast supports the widest range of local payment methods at 3.2% + R2 for cards. Shopify merchants pay an additional 0.6–2.0% on top of the gateway rate depending on their plan. The cheapest option depends on your payment mix, order volume, and payout frequency — not just the advertised card rate.
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Get a Free Checkout ReviewWhat Do South African Payment Gateway Fees Actually Cover?
A payment gateway's fee structure in South Africa typically has five components, and the monthly cost you actually pay depends on all of them — not just the one percentage advertised on the pricing page.
| Fee Component | What It Is | Who Charges It |
|---|---|---|
| Transaction rate (%) | Percentage of each transaction value | All gateways |
| Flat fee per transaction (R) | Fixed rand amount charged per sale, regardless of order value | PayFast, Peach Payments |
| Monthly account fee | Fixed monthly cost to maintain your merchant account | PayGate (R99) |
| Payout fee | Cost to transfer settled funds to your bank account | PayFast (R8.70 standard; 0.8% immediate) |
| Refund fee | Cost to process a customer refund | PayFast (R2.00 ex VAT) |
The flat fee per transaction is the component that most merchants underestimate. At a R250 average order value on PayFast, the R2.00 flat fee adds 0.8% on top of the 3.2% rate — making the effective card rate 4.0%. At a R1,000 average order value, that flat fee is only 0.2%, making the effective rate 3.4%. Gateway economics look different at a R250 average order than at a R1,000 average order.
Key Takeaway
The flat fee per transaction punishes low-order-value stores more than high-order-value stores. If your average basket is under R200, the flat fee component can add 1%+ to your effective transaction rate. Run the full cost calculation, not just the percentage comparison.
Payment Gateway Fees Comparison South Africa: 2026 Rate Tables
The payment gateway fees comparison South Africa table below covers mid-2026 published rate schedules for six gateways. All rates are exclusive of VAT; high-volume merchants at most providers can negotiate custom rates beyond these standard tiers.
| Gateway | Card Rate | EFT Rate | Monthly Fee | Settlement | Best For |
|---|---|---|---|---|---|
| PayFast | 3.2% + R2.00 | 2.0% (min R2) | R0 | Next day | Widest payment method coverage (18+ options) |
| Peach Payments | 2.95% + R1.50 | 1.5% + R1.50 | R0 | Next day | Lower rates on both cards and EFT |
| Yoco | 2.95% | Not offered | R0 | T+2 | Card-heavy stores, in-person + online split |
| Ozow | Not offered | 1.5% | R0 | Instant–next day | EFT-specialist; lowest EFT rate |
| Stitch | 2.95% | 2.0% (Capitec) | R0 | ~1 day | Growing card + Capitec Pay coverage |
| PayGate (DPO) | 3.5% | 1.5% | R99 | T+2 to T+3 | Established enterprise accounts |
Sources: PayFast fees page (direct, fetched mid-2026); other providers from the ECD Payment Gateway Comparator, mid-2026. All rates ex VAT. Verify current rates directly with each provider — they update periodically.
A few important caveats on the table above:
- Yoco and Ozow are specialists. Yoco doesn't natively offer Instant EFT; Ozow doesn't offer card acceptance. If your checkout needs both, you'd pair one of these with a complementary gateway or choose a full-coverage provider (PayFast, Peach, Stitch).
- PayFast custom pricing becomes available above R50,000 monthly GMV. Contact their merchant team directly for volume pricing.
- PayGate's R99/month only makes economic sense once your monthly transaction volume is high enough to absorb it. At R10,000/month, that fee alone adds 1% to your effective rate.
For a detailed two-way head-to-head, see our PayFast vs Peach Payments fee comparison which runs the scenarios side by side at three volume levels.
How Your Payment Mix Changes the Real Monthly Cost
The table above shows per-transaction rates, but the rate that matters is your blended monthly cost as a percentage of GMV. That number changes significantly depending on whether your customers pay mostly by card, mostly by EFT, or a mix of both.
The worked example below uses a hypothetical South African store processing R100,000/month GMV across approximately 400 transactions (average order value ~R250), with cards covering R80,000 and EFT covering R20,000 of the monthly volume — a card-heavy mix common in SA ecommerce. All figures are computed from mid-2026 published rates and are exclusive of VAT. Your actual costs will differ based on your order value, transaction count, payment mix, and payout frequency.
Worked Example: R100,000/Month Store (Card-Heavy Mix)
PayFast: Cards (R80k) → 3.2% = R2,560 + 320 txns × R2 = R640 → R3,200. EFT (R20k) → 2.0% = R400. Payouts (4 × R8.70) = R35. Total ≈ R3,635/month.
Peach Payments: Cards (R80k) → 2.95% = R2,360 + 320 × R1.50 = R480 → R2,840. EFT (R20k) → 1.5% = R300 + 80 × R1.50 = R120 → R420. Payouts included. Total ≈ R3,260/month.
Stitch: Cards (R80k) → 2.95% = R2,360. EFT/Capitec (R20k) → 2.0% = R400. Total ≈ R2,760/month.
PayGate: Cards (R80k) → 3.5% = R2,800. EFT (R20k) → 1.5% = R300. Monthly fee R99. Total ≈ R3,199/month.
Figures computed from mid-2026 published rate schedules (ex VAT). For EFT-only, Ozow at 1.5% on R20k = R300 (must pair with a card solution). For card-only stores, Yoco at 2.95% on R80k = R2,360.
What the worked example shows: at R100,000/month with a typical SA card/EFT mix, the cheapest full-coverage option in this sample is Stitch at ~R2,760/month — roughly R875 less than PayFast and R440 less than Peach Payments. But Stitch's EFT coverage is currently Capitec Pay only; if your customers use a wider spread of SA banks for EFT, Peach Payments' broader Pay by Bank offering may be worth the difference.
The annual impact scales: a R875/month saving is R10,500/year. For most sub-R200,000/month stores, that difference is meaningful but should be weighed against integration stability, payment method breadth, and settlement reliability.
Key Takeaway
As a working rule of thumb: once EFT accounts for a meaningful share of your checkout mix — say, roughly a third or more of transactions — the EFT rate matters as much as the card rate. Ozow's 1.5% EFT rate is the lowest in the market, but it needs to be paired with a card gateway. Peach Payments at 1.5% + R1.50 on EFT is competitive for merchants who want a single integrated solution handling both.
Beyond the Headline Rate: Payout Fees, BNPL Premiums, and Refunds
A complete payment gateway fees comparison South Africa merchants can act on goes beyond the rate column. Three cost components regularly surprise SA merchants who calculated their costs from the advertised rate alone.
Payout fees
PayFast charges R8.70 ex VAT per standard payout to your bank account. A store that triggers payouts weekly pays ~R35/month; a store on daily payouts pays ~R174/month. PayFast also offers immediate (same-day) payouts at 0.8% of the payout value (minimum R14 ex VAT) — at R50,000 a month in settlements, that's R400/month just in payout fees if you're using instant settlement.
Peach Payments settled automatically on the next business day with no payout fee on the standard plan. Stitch and Ozow also include settlement without a per-payout charge on their published plans. If cash flow speed matters to your operation, factor payout fee structure into the full cost — not just the transaction rate.
BNPL premiums
If you offer buy now, pay later through PayFast, the rates are significantly higher than standard card rates: buy now pay later in South Africa via PayFast costs 5.45% + R5.00 (Payflex) or 5.5% + R2.00 (MoreTyme) per transaction. At a R500 average BNPL order, the Payflex fee alone is R32.25 — versus R18.00 for the same transaction on a standard card. BNPL conversion uplift needs to cover that premium before it improves your net margin.
Refund fees
PayFast charges R2.00 ex VAT per refund. For stores with a 5% return rate on 400 transactions/month, that's an extra R40/month. It's a small number in isolation, but it's real cost that compounds at scale and doesn't appear on the rate card comparison.
Common mistake: Choosing a gateway based on a card rate comparison table without checking payout frequency costs. A merchant on PayFast who triggers daily payouts at R8.70 each pays R174/month in payout fees — equivalent to adding ~0.17% to the effective rate at R100,000/month GMV.
Shopify Merchants: The Additional Transaction Fee Layer
South African Shopify merchants face a cost layer that doesn't appear in any gateway's pricing: Shopify's own third-party transaction fee. Because Shopify Payments is not available in South Africa, every transaction processed through a third-party gateway incurs an additional Shopify fee — 2.0% on Basic, 1.0% on Shopify (Standard), and 0.6% on Advanced.
| Shopify Plan | Shopify's Additional Fee | Combined with PayFast Cards | Combined with Peach Cards |
|---|---|---|---|
| Basic | 2.0% | 5.2% + R2 per txn | 4.95% + R1.50 per txn |
| Shopify (Standard) | 1.0% | 4.2% + R2 per txn | 3.95% + R1.50 per txn |
| Advanced | 0.6% | 3.8% + R2 per txn | 3.55% + R1.50 per txn |
Combined rates computed from Shopify third-party fees and mid-2026 published gateway rates, ex VAT.
The implication: a Shopify merchant on the Basic plan using PayFast for card transactions is paying 5.2% + R2 on every sale before VAT. At a R500 average order value, that's R28 per transaction. Moving to the Advanced plan with Peach Payments brings the same sale to R19.25 — a R8.75 saving per transaction, or R8,750 on 1,000 transactions.
The Advanced plan costs more per month in subscription fees, so you need sufficient volume for the reduced transaction fee to offset that fixed cost. For context on where that crossover sits, see our Shopify plan costs in South Africa breakdown.
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Get a Margin CalculationWhy South African Businesses Choose Growth Pulse Media
Most ecommerce growth advice stops at "choose the right gateway" — but the gateway decision is one node in a larger checkout and margin optimisation problem. Dirk founded Growth Pulse Media after running SA ecommerce operations first-hand: paying the invoices, reviewing the gateway reconciliations, and watching checkout drop-off metrics move in real time. That operational background is what our Shopify marketing agency brings to every client engagement.
When we review a store's payment setup, we're looking at gateway cost against average order value, EFT vs card split, Shopify plan tier, BNPL adoption rates, and settlement timing against the store's cash flow cycle — all at once. We work with PayFast, Peach Payments, Yoco, and Ozow integrations across Shopify stores. We keep our client load deliberately limited so that analysis is senior-level, not templated.
If your checkout conversion rate is below what the industry benchmarks suggest for your category, the gateway cost structure is one of six things we examine — and it's rarely the only lever.
Who This Post Is NOT For
Stores processing over R500,000/month. At high volume, published rate cards are a starting point for negotiation, not a final number. Every major SA gateway offers custom enterprise pricing above this threshold. This post covers standard published rates only.
Merchants who primarily accept in-person payments. Yoco's card machine rates and Ozow's QR payment setup for physical retail follow different fee logic than online checkout. If most of your revenue is point-of-sale, this comparison won't give you your real numbers.
Businesses processing payments in foreign currencies. Cross-border checkout on a South African gateway adds currency conversion fees on top of the transaction rate — and those fees can add meaningful cost per transaction. If you're selling internationally from South Africa, see our cross-border ecommerce guide before committing to a gateway.
Merchants who haven't locked down their Shopify plan first. The gateway decision and the Shopify plan decision are linked. Choosing a gateway before deciding your plan tier means you may optimise for a cost that changes when you upgrade or downgrade. Nail the plan decision, then the gateway.
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Book a Checkout AuditFrequently Asked Questions
What is the cheapest payment gateway in South Africa?
For EFT-only transactions, Ozow at 1.5% is the lowest published rate in the South African market. For a full checkout covering both cards and EFT, Stitch (2.95% cards, 2.0% Capitec EFT) and Peach Payments (2.95% + R1.50 cards, 1.5% + R1.50 EFT) are the most competitive on standard published rates. The cheapest option for your store depends on your payment method mix, average order value, and payout frequency — not just the headline percentage.
Do South African Shopify merchants pay extra transaction fees on top of gateway fees?
Yes. Because Shopify Payments is not available in South Africa, Shopify charges an additional third-party transaction fee on every sale: 2.0% on the Basic plan, 1.0% on the Standard (Shopify) plan, and 0.6% on Advanced. This fee stacks on top of whatever your payment gateway charges, meaning the combined card rate on Basic with PayFast is approximately 5.2% + R2 per transaction.
How does PayFast compare to Peach Payments on fees?
Peach Payments is cheaper on both card and EFT rates compared to PayFast's standard published rates: 2.95% + R1.50 for cards versus PayFast's 3.2% + R2, and 1.5% + R1.50 for EFT versus PayFast's 2.0%. PayFast's advantage is breadth — it supports more than 18 local payment methods including SnapScan, Zapper, Payflex, and MoreTyme. For a detailed worked example at multiple volume levels, see our PayFast vs Peach Payments comparison.
What are BNPL payment fees in South Africa?
Buy now, pay later through PayFast carries a significantly higher rate than standard card transactions. Payflex costs 5.45% + R5.00 per transaction; MoreTyme costs 5.5% + R2.00. Both rates are exclusive of VAT. Other BNPL providers such as Mobicred charge 3.2% via PayFast. The rate premium over a standard PayFast card transaction is more than 2 percentage points on the rate alone — the conversion uplift BNPL generates needs to exceed that margin cost before it improves net profitability.
How quickly do South African payment gateways settle funds?
Settlement times vary by gateway. Peach Payments settles next business day automatically. Stitch settles in approximately one business day. Ozow settles instantly to next day. PayFast settles next business day (standard payouts at R8.70 each; same-day payouts available at 0.8% of the payout value). PayGate (DPO) settles T+2 to T+3. Settlement speed matters for working capital — a T+3 gateway at high volume ties up more cash than a T+1 or next-day provider.
Get the Right Gateway for Your Store's Actual Numbers
Growth Pulse Media works with Shopify stores across South Africa on PayFast, Peach Payments, Yoco, and Ozow integrations. We review your checkout cost structure — gateway rate, Shopify plan tier, payout fee, payment mix — and tell you exactly what's worth changing and what's not. No jargon, no templated advice. No obligation — we'll get back to you within 24 hours.
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