Payment Gateways

Merchant Fees Comparison South Africa: What Every Business Actually Pays

Alister

E-commerce Consultant

| 6 Aug 2026 16 min

What "merchant fees" actually means

Merchant fees (also called payment processing fees or the merchant discount rate) are everything you pay to accept money. For a South African online business in 2026, that typically means:

The gateway's percentage + flat fee (the biggest line)
The platform's third-party fee on Shopify (because Shopify Payments isn't available in SA)
Any monthly plan or hardware fees (Yoco online plans, card machines)
VAT on all of the above
Occasional extras like BNPL fees, PCI compliance fees or chargeback fees

Most business owners only know the first number — the percentage. This guide breaks down every line, shows you the real mid-2026 SA rates, and models what a R100,000-a-month business actually pays across gateways and platforms.

Quick answer: South African merchant fees typically cost 2.85% to 3.2% plus R1-R2 per card transaction, and 1.5% to 2% for pay-by-bank/EFT (mid-2026 rates). On Shopify you must add the platform's third-party payment provider fee — 2% on Basic, 1% on Grow, 0.6% on Advanced, 0.2% on Plus — because Shopify Payments isn't available in South Africa. All fees are ex-VAT (15%). For a R100k/month Shopify Basic store, realistic all-in processing is roughly R4,900-R5,700; moving customers to pay-by-bank can cut that to about R3,500. The biggest lever isn't the sticker rate — it's your card-versus-EFT mix and negotiating at volume.

How percentage and flat fees work

A gateway fee has two parts:

The percentage (interchange-driven). The gateway pays Visa, Mastercard or AMEX interchange and passes it through with its own margin. That's why the percentage barely varies between gateways — the card schemes set the floor. Published SA rates in 2026: Ozow 2.85%, Yoco 2.95%, Stitch 2.95%, Peach ~2.95%, Paystack 2.9% + R1, PayFast 3.2% + R2.

The flat fee. R1 (Paystack), R1.50 (Peach) or R2 (PayFast) per transaction, covering the scheme's fixed authorisation cost. It's tiny per order but decisive at low order values:

Key fact: At a R150 average order value, a R2 flat fee is equivalent to an extra 1.33% on the rate. On 2,000 orders a month, it's R4,000 in fees alone (figures from gateway fee sheets, 2026).

The maths for one transaction:

Cost of one card payment =
  (Order value × gateway %) + flat fee

So a R400 order on PayFast costs (R400 × 3.2%) + R2 = R14.80 — effectively 3.7% of the order. The same order on Yoco costs R11.80 — 2.95%. On small orders the flat fee makes cheap gateways expensive and expensive gateways brutal.

The real South African gateway rates (2026)

Mid-2026 published rates, ex-VAT, from the verified CrazyClicks fee sheet:

Gateway	Card rate	Flat fee	EFT / Pay-by-Bank	Monthly fee	Notes
PayFast (Payfast by Network)	3.2%	R2	2.0% + min R2	None	Rate dropped from 3.5% on 1 June 2026
Paystack	2.9% local / 3.1% intl	R1	2.0% EFT	None	Stripe-owned, developer-friendly
Yoco	2.95% local / 3.40% intl	None	Not offered	R0 / R249 / R499	2.55% on paid plans; POS hardware
Peach Payments	~2.95% local / ~3.50% intl	R1.50	Capitec Pay	None	Real-time payouts ~90 sec
Stitch	2.95%	None	2.0% Capitec Pay	None	Built for Shopify; BNPL May 2026
Ozow	2.85% (tiered)	Per-method	1.5%	None	Cheapest pay-by-bank in SA
PayGate (DPO)	Negotiated	Negotiated	SiD Secure EFT	Negotiated	Enterprise, own merchant account

Key fact: All these figures are ex-VAT. Add 15% for a non-VAT-registered business. A PayFast "3.2%" rate is really 3.68% with VAT for unregistered sellers.

Shopify's stacked third-party fee

This is the fee that quietly breaks South African budgets. Because Shopify Payments is not available in South Africa, every local Shopify merchant must use a third-party gateway — and Shopify charges an extra "third-party payment provider" fee on every sale:

Shopify plan	Third-party fee	Plus a typical gateway rate	Combined (card)
Basic	2.0%	PayFast 3.2% + R2	~5.2-5.5%
Grow (was "Shopify")	1.0%	Peach ~2.95% + R1.50	~3.95%
Advanced	0.6%	Negotiated ~2.4%	~3.0%
Plus	0.2%	Negotiated	~2.6%

Key fact: On Shopify Basic with PayFast, card payments cost about 5.2% to 5.5% all-in — more than double what the gateway advertises. Combined with a monthly subscription of ~R450-R730 and ~R700-R1,400 for essential apps, a R100k/month store realistically spends R5,500-R8,500 a month on platform and processing costs — a 6-8% bite out of revenue (Shopify pricing and gateway fee sheets, July 2026).

The advanced-tier trick: if you're on Shopify Grow (1%) or Advanced (0.6%), the platform fee shrinks dramatically, and a negotiated gateway rate can bring combined card costs down to ~3%.

Card schemes: Visa, Mastercard and AMEX

The percentage you pay is mostly pass-through of card scheme interchange, which is why gateways cluster in the same range:

Visa and Mastercard carry near-identical interchange in South Africa and are priced almost the same by every gateway (2.85-3.2%).
American Express has different, typically higher interchange. Gateways often price AMEX separately, and some don't accept it at all. If you want to display "We accept AMEX", check your gateway's specific AMEX rate first — it's usually a few tenths of a percent higher than Visa/Mastercard.
International cards cost more everywhere: Paystack 3.1% + R1, Yoco 3.40%, Peach ~3.50%.

Your takeaway: you can't negotiate interchange away with the gateway. What you can influence is your method mix (EFT vs card) and your volume pricing.

EFT vs card economics

The single biggest fee lever in South Africa is the choice between card and EFT rails:

Payment method	Gateway rate	Why it's different
Card (Visa/MC)	2.85-3.2% + R1-R2	Includes interchange paid to the card scheme
Pay-by-bank (Ozow)	1.5%	No interchange — moves money directly between bank accounts
Instant EFT (PayFast)	2.0% + min R2	Bank redirection without interchange
Capitec Pay (Stitch)	2.0%	Bank-level direct debit

At R100k/month, a 50/50 card/EFT split saves roughly R1,000-R1,500 a month versus all-card, without losing a single sale — as long as you offer the EFT option prominently. On Shopify Basic, Ozow Pay-by-Bank is about 3.5% all-in versus ~5.2-5.5% for PayFast cards.

Key fact: Moving half of a R100k/month store's volume from card (3.2%) to pay-by-bank (1.5%) cuts processing fees by roughly R850 a month on the gateway line alone — over R10,000 a year (based on mid-2026 rates).

The honest trade-off: not every customer will use EFT, and high-trust card checkout still converts best for impulse purchases. The winning stores design their checkout to offer both and nudge high-AOV customers toward EFT.

BNPL fees and the conversion trade-off

Buy now, pay later (BNPL) arrived for SA merchants via Stitch in May 2026. BNPL typically carries a higher merchant fee than standard cards because the BNPL provider fronts the funds and carries the risk.

Pros: higher conversion and average order value, especially on R1,500+ products.
Cons: an extra fee per BNPL transaction, plus integration work.

Before enabling BNPL, ask for the specific rate card and model it: if BNPL raises AOV by 20% but costs 2% more than cards, it can still be profitable — but only if you price it into the product, not swallow it.

Monthly, PCI and hardware fees

Beyond per-transaction costs:

Monthly plan fees. Yoco's paid online plans: R249/month (Plus) or R499/month (Pro) — both drop the card rate to 2.55%. Worth it roughly once you process enough that the rate drop exceeds the plan fee.
Hardware. If you sell in person, Yoco card machines involve a purchase or rental cost on top of processing.
PCI/compliance. Most SA aggregator gateways bundle PCI DSS compliance into their pricing, but enterprise setups may charge separately. Ask.
Chargebacks. Dispute fees and the cost of losing a chargeback are real and usually unadvertised.

VAT on merchant fees

All the rates above are quoted ex-VAT. South African VAT is 15%.

VAT-registered: you charge VAT on your sales and reclaim input VAT on your fees. Your real processing cost is about 87% of the sticker.
Not registered: the full 15% hits you. A 2.9% fee is really 3.335%.

This single line changes gateway rankings for unregistered businesses, so don't skip it.

Worked example: total monthly fees for a R100k business

Let's model a realistic store: R100,000/month, 250 orders, R400 average order value.

On Shopify Basic (2% third-party fee)

Gateway	Card (all 100%)	Shopify 2%	Total
PayFast (3.2% + R2)	R3,200 + R500 = R3,700	R2,000	R5,700
Paystack (2.9% + R1)	R2,900 + R250 = R3,150	R2,000	R5,150
Peach (~2.95% + R1.50)	R2,950 + R375 = R3,325	R2,000	R5,325
Yoco (2.95%)	R2,950	R2,000	R4,950
Stitch (2.95%)	R2,950	R2,000	R4,950
Ozow cards (2.85%)	R2,850	R2,000	R4,850
Ozow Pay-by-Bank (1.5%)	R1,500	R2,000	R3,500

With a realistic 60% card / 40% EFT mix on Ozow: (R60,000 × 2.85%) + (R40,000 × 1.5%) + R2,000 = R1,710 + R600 + R2,000 = R4,310.

On WooCommerce (no third-party fee)

Gateway	Card (all 100%)	Total
PayFast	R3,700	R3,700
Paystack	R3,150	R3,150
Peach	R3,325	R3,325
Yoco	R2,950	R2,950
Stitch	R2,950	R2,950
Ozow cards	R2,850	R2,850
Ozow EFT	R1,500	R1,500

With VAT (non-registered, all-card Shopify)

The same PayFast total becomes R5,700 × 1.15 = R6,555. VAT-registered? You reclaim it — but only with proper records.

Key fact: For a R100k/month store, the difference between the best and worst realistic setup is roughly R2,200 a month — more than R26,000 a year — with zero change in sales. Full breakdown: see our payment gateway comparison guide.

Shopify vs WooCommerce: fee comparison

Cost line	Shopify (Basic)	WooCommerce
Platform subscription	~R450-R730/mo	Free (but hosting ~R100-R400/mo)
Third-party transaction fee	2%	None
Gateway fees	Same rates	Same rates
Essential plugins/apps	~R700-R1,400/mo	Plugins mostly free one-offs; premium ones add up
Total processing on R100k (PayFast)	~R5,700	~R3,700

WooCommerce saves you the 2% Shopify surcharge (~R2,000/month at R100k), but you trade it for hosting, maintenance and more hands-on management. Our full Shopify vs WooCommerce breakdown covers the non-fee trade-offs like security, apps and scalability.

How to negotiate better rates

The published rates are a starting point, not the ceiling:

Build your volume case. Bring your modelled monthly gateway spend (the table above) to the negotiation.
Approach Peach Payments at R200k+. They quote custom rates for merchants processing roughly R200k or more a month — at R500k/month, a negotiated ~2.4% card rate can save R3,000+/month versus PayFast.
PayGate for enterprise. If you have your own internet merchant account and enterprise volume, everything is negotiable.
Use the Shopify plan lever. Moving from Basic (2%) to Grow (1%) or Advanced (0.6%) shrinks the platform fee — sometimes cheaper than arguing with a gateway.
Ask about downgrade terms. Get written confirmation of what happens to your rate if volume dips.
Put Yoco's paid plan to the test. 2.55% on Plus/Pro only pays off if the rate drop beats the R249/R499 monthly fee — do the maths at your volume.
Re-quote yearly. The SA market moved in 2026 (PayFast 3.5% → 3.2%); incumbents adjust pricing when pushed.

Beginner mistakes to avoid

Budgeting on the sticker rate. The flat fee, Shopify surcharge and VAT often double the headline number.
Ignoring the EFT lever. Refusing to offer pay-by-bank on a high-AOV store is leaving 1.5-2% of every sale on the table.
Not claiming input VAT. VAT-registered businesses that don't reclaim input VAT on gateway fees are donating 15% of their processing cost.
Staying on the wrong Shopify plan. If you're processing R200k+/month on Basic at 2%, the Advanced plan's 0.6% fee can pay for itself.
Accepting the first rate you're quoted. Nobody at Peach or PayGate says no if you never ask.
Ignoring settlement speed. Slow settlement ties up working capital that has a real opportunity cost.
Enabling BNPL without modelling it. A 2% extra fee on BNPL orders must be priced into the product.
Never reviewing fees. Rates changed twice in the last year; an annual re-quote keeps you current.

Expert tips

Design the checkout for EFT nudges. On orders above R2,000, make Pay-by-Bank the highlighted option — cheaper for you, preferred by many SA buyers.
Track effective rate monthly. Divide total gateway spend by sales. If it drifts above ~4% on Shopify Basic, you have a mix or fee problem.
Negotiate with numbers. A spreadsheet of your modelled spend is the strongest opening line in any rate conversation.
Beware the flat-fee trap at low AOV. Under R200 AOV, a R2 flat fee outweighs most rate differences — Yoco and Stitch (no flat fee) tend to win there.
Reclaim input VAT diligently. Keep gateway invoices; your SARS file needs them for the R2.3m threshold era (registration threshold raised on 1 April 2026).
Use a fallback gateway. A second gateway is cheap insurance against outages that stop your store from earning entirely.
Model every gateway on the same spreadsheet. Our best payment gateway guide gives you the full table to copy.

The quick-start checklist

Pulled monthly sales, order count and average order value
Estimated your card/EFT/BNPL mix
Listed every gateway's %, flat fee and monthly fee
Added Shopify's third-party fee (2% / 1% / 0.6% / 0.2%)
Adjusted for VAT (reclaim if registered, add 15% if not)
Included monthly plan, hardware and PCI fees
Compared WooCommerce vs Shopify fee structures
Requested a custom rate quote at R200k+ volume
Checked settlement speed against cash-flow needs
Enabled EFT/pay-by-bank prominently at checkout
Set up a fallback gateway
Scheduled an annual fee re-quote

South African case study

Illustrative example, not a real client.

The business: A Gqeberha online health-supplements brand on Shopify Grow (1% third-party fee). Monthly sales R320,000; 1,100 orders; average order value R290; 85% card, 15% EFT; using PayFast exclusively.

The problem: At R290 AOV, the R2 flat fee was brutal: (R320,000 × 3.2%) + (1,100 × R2) = R10,240 + R2,200 = R12,440 in gateway fees, plus R3,200 Shopify Grow fee — about R15,640 a month, nearly 4.9% of revenue.

The fix: CrazyClicks re-modelled the whole stack. The store switched to Yoco (2.95%, no flat fee) for cards and Paystack as fallback, and added Ozow Pay-by-Bank at checkout for orders over R250. The EFT share climbed to 40%.

The result: New monthly cost: cards (R192,000 × 2.95% = R5,664) + EFT (R128,000 × 1.5% = R1,920) + Shopify Grow (R3,200) = R10,784 — a saving of about R4,856 a month (R58,000 a year). The no-flat-fee gateway also eliminated the per-order penalty on low-AOV orders.

The lesson: at low average order values the flat fee is the silent killer, and EFT rails are the cheapest fix. Fee audits pay for themselves within the first month.

Frequently asked questions

Q: What are typical merchant fees in South Africa? A: 2.85-3.2% plus R1-R2 per card transaction and 1.5-2% for pay-by-bank/EFT (mid-2026). Add the 15% VAT if not registered, and Shopify's third-party fee (2% Basic, 1% Grow, 0.6% Advanced) if applicable.

Q: How much does Shopify cost in merchant fees in South Africa? A: On top of the subscription, Shopify charges 2% (Basic), 1% (Grow), 0.6% (Advanced) or 0.2% (Plus) per transaction because Shopify Payments isn't available in SA. Gateway fees are additional.

Q: Are EFT payments cheaper than card payments? A: Yes — roughly half the cost. Pay-by-bank is 1.5-2% versus ~3% for cards. A 50/50 split on a R100k store typically saves R1,000-R1,500 a month.

Q: What is the cheapest way to accept payments in South Africa? A: Ozow Pay-by-Bank at 1.5%, then Ozow cards (2.85%) and Yoco (2.95%). On Shopify Basic, Ozow Pay-by-Bank is ~3.5% all-in versus ~5.2-5.5% for PayFast cards.

Q: Are merchant fees VAT-able? A: Yes, ex-VAT at 15%. VAT-registered businesses reclaim input VAT (~87% effective cost); others must add the 15%.

Q: Can I negotiate merchant fees? A: Yes. Peach Payments at ~R200k+/month, PayGate for enterprise, and Yoco paid plans (2.55%). Bring your modelled spend to the call.

Q: How do Visa, Mastercard and AMEX compare? A: Visa and Mastercard are priced near-identically. AMEX carries higher interchange and is usually priced separately and higher.

Q: What is Shopify's third-party fee? A: The extra fee Shopify charges because you can't use Shopify Payments in SA: 2% Basic, 1% Grow, 0.6% Advanced, 0.2% Plus, on every transaction, stacked on top of your gateway rate.

Q: How much does it cost to run a R100,000 store in South Africa? A: R5,500-R8,500 a month all-in on Shopify Basic (subscription, third-party fee, gateway, apps, domain) — roughly 6-8% of revenue.

Q: Is WooCommerce cheaper than Shopify for fees? A: On processing fees, yes — no third-party transaction fee saves ~R2,000/month at R100k. But you pay for hosting, plugins and maintenance instead.

Summary

South African merchant fees are a stacked cost: gateway percentage + flat fee + Shopify third-party fee + VAT, with settlement and payment-method mix affecting the real number. The verified 2026 rates show that card acceptance costs 2.85-3.2%, EFT costs 1.5-2%, and Shopify's surcharge adds 0.2-2%. For a R100k/month store the realistic range is R3,500 to R5,700 a month — and the cheapest path is usually EFT adoption plus negotiating at volume.

Key takeaways

Cards cost 2.85-3.2% + R1-R2; pay-by-bank costs 1.5-2% — EFT is your biggest fee lever.
Shopify stacks 2% (Basic), 1% (Grow), 0.6% (Advanced) on every third-party gateway transaction.
All fees are ex-VAT; claim input VAT if registered, budget 15% extra if not.
At R100k/month, gateway choice moves costs by R2,200/month or more.
Negotiate with Peach at R200k+ and re-quote annually — SA rates dropped twice in the past year.

Sticky sidebar: CrazyClicks services card (link to /services).

Ready to cut your processing fees?

CrazyClicks is a full-service digital agency in Cape Town. We audit merchant fees, reconfigure gateways, redesign checkouts for EFT adoption, and build or migrate Shopify and WooCommerce stores. Start a project, see our services, or read our case studies.

Building new on Shopify? It's SA's most popular ecommerce platform — 22,000+ active stores and growing ~28% year-on-year — and its ecosystem makes gateway setup painless. Launch your online business today and claim the current introductory offer where it's active. (Affiliate link — we may earn a commission at no extra cost to you.)

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Alister

at CrazyClicks