Shopify with PayFast: Setup Guide & True Costs (2026)
You've chosen Shopify — smart. Now you need to get paid. And in South Africa, the single most popular way for small stores to do that is PayFast, the gateway that's been powering local online payments for nearly two decades and now runs under Network International as Payfast by Network.
But here's the trap: the PayFast fee table you'll find on its website is only half the story. On Shopify, every sale through PayFast also carries Shopify's own third-party provider fee — because Shopify Payments isn't available in South Africa. If you don't stack those costs correctly, you'll price your products wrong and watch margin disappear.
This guide gives you the complete, verified 2026 picture: what PayFast costs, exactly how to connect it to Shopify in a native integration, when you'll actually see your money, and how a simple switch to Instant EFT can cut your payment costs by more than a third.
Quick answer: PayFast (now Payfast by Network) is the most popular payment gateway for South African Shopify stores. Its verified mid-2026 fees are 3.2% + R2 per card payment, 2% + min R2 for Instant EFT, with no monthly fee. It integrates with Shopify via a native app in under 15 minutes. Because Shopify Payments is unavailable in SA, Shopify adds its own fee on top — 2% on Basic, 1% on Grow, 0.6% on Advanced — so a card sale on a Basic plan really costs about 5.2–5.5% combined. PayFast settles in 2 business days, or immediately for a 0.8% fee. Pushing customers toward Instant EFT is the single biggest cost saver.
Setting up your store or payments and want it done right? Get expert help from CrazyClicks → contact us.
What is PayFast?
PayFast is a South African payment gateway launched in 2007 that lets online stores accept cards, Instant EFT, and alternative payment methods without needing your own merchant account with a bank. You sign up, get approved, and start taking payments — no bank negotiation, no minimum turnover. The Network International deal: PayFast was acquired by Network International, a Dubai-based payments group, and now trades as Payfast by Network. The most visible benefit for merchants so far: the standard card fee dropped from 3.5% + R2 to 3.2% + R2 on 1 June 2026. The acquisition has also expanded PayFast's acquiring capacity and scale, which matters as it processes a meaningful share of South Africa's small-store e-commerce volume.
Key fact: PayFast is a POPIA-conscious, PCI-DSS-compliant gateway — card details never touch your server, which keeps your POPIA compliance obligations simpler and reduces your PCI-DSS scope.
Why PayFast + Shopify works well in SA
- Native Shopify integration. No developer needed. The PayFast app in the Shopify App Store handles cards, Instant EFT, SnapScan, Zapper, Mobicred and more in one install.
- No monthly fee. Unlike a card-machine business, PayFast doesn't charge you for existing. Great for a new store with thin volume.
- Widest local method coverage. Instant EFT works across the big South African banks, which captures buyers who don't pay by card.
- Recurring billing. Subscriptions and payment plans are supported, useful for membership and coaching businesses.
- Rand-native. Pricing, settlements and invoices are all in Rands, so no currency surprises.
PayFast fees in 2026 (verified)
The following are PayFast's published standard fees as of mid-2026 (excluding VAT):
| Method | Fee | Notes |
|---|---|---|
| Card payments | 3.2% + R2 | Reduced from 3.5% + R2 on 1 June 2026 |
| Instant EFT / Capitec Pay | 2.0% + min R2 | Cheapest mainstream method PayFast offers |
| SnapScan / Zapper / Mobicred | Supported via PayFast's standard fee structure | Great for mobile-first shoppers |
| Monthly fee | None | No subscription on the standard account |
| Immediate payout | 0.8% of amount | Option to skip the 2-business-day wait |
| Settlement fee (standard) | None | Standard 2-business-day payout is free |
Worked example on a R1,000 card sale: PayFast takes 3.2% (R32) + R2 = R34. On Instant EFT: 2% (R20) + min R2 = R22. The R12 difference per R1,000 might look small — multiply it by 300 orders a month and it's R3,600 a year on every R1,000 of basket value.
The true stacked cost on every Shopify plan
Here's the part most blog posts skip. Because Shopify Payments isn't available in South Africa, Shopify charges a third-party payment provider fee on every sale processed through PayFast (or any external gateway):
| Shopify plan | Approx ZAR/month (monthly billing) | Shopify third-party fee | PayFast card combined | PayFast Instant EFT combined |
|---|---|---|---|---|
| Basic | ~R450 | 2.0% | ~5.2–5.5% | ~4.0% |
| Grow (was "Shopify") | ~R1,170 | 1.0% | ~4.2–4.5% | ~3.0% |
| Advanced | ~R7,200 | 0.6% | ~3.8–4.1% | ~2.6% |
| Plus | from ~R41,000 | 0.2% | ~3.4–3.7% | ~2.2% |
The combined figures assume the R2 per-transaction fee works out to roughly 0.2–0.5% depending on your order value. On a store doing R100,000 a month on Basic with 250 card orders, the real cost is roughly:
- Shopify subscription: ~R450–R730
- Shopify third-party fee (2%): ~R2,000
- PayFast card fees (3.2% + R2): ~R3,700
- Payment + subscription total: ~R6,150–R6,430 a month
Now switch those same 250 orders to Instant EFT where possible:
- PayFast Instant EFT (2% + min R2): ~R2,500
- Saving vs cards: ~R1,200 a month, ~R14,400 a year
And moving from Basic to Grow (1% Shopify fee) on a card-heavy store drops the Shopify fee from R2,000 to R1,000 — which more than pays for the higher subscription. Our complete breakdown of plan economics is in Shopify pricing in South Africa, and the wider platform-vs-platform picture in the Shopify vs WooCommerce showdown.
How to integrate PayFast with Shopify (step by step)
Prerequisites: a PayFast merchant account in good standing and a Shopify store on any paid plan (Starter works too). You don't need a developer.
- Create your PayFast account. Go to payfast.co.za, register as a business or individual, and complete the verification — you'll need your ID/company details and a bank account for payouts. Approval typically takes 1–3 business days.
- Grab your API credentials. Log into the PayFast dashboard, go to Settings, and copy your Merchant ID and Merchant Key.
- Install the PayFast Shopify app. In your Shopify admin, go to Apps → Shopify App Store, search "PayFast", and click Add app.
- Enter your credentials in Shopify. Open the PayFast app from your Apps list, paste the Merchant ID and Merchant Key, and save. The app will map your PayFast methods into the checkout automatically.
- Activate PayFast in Settings → Payments. Under Payment providers, ensure PayFast shows as active. Tick the methods you want visible: cards, Instant EFT, SnapScan, Zapper, Mobicred, Capitec Pay.
- Configure your order status mapping. In the PayFast app settings, confirm that successful payments mark orders as Paid (not Pending) so fulfilment isn't delayed.
- Run test orders. Place a R1 test order on desktop and mobile. Pay by card, then by Instant EFT, and confirm both complete and reflect as paid in Shopify.
- Go live and monitor. Check your first real payouts, reconcile them against Shopify orders, and keep an eye on the payment logs for failed methods.
If you'd rather not do this yourself — or want it done with proper fraud rules, POPIA notices and tax mapping — CrazyClicks offers Shopify development and can handle the integration end to end.
Settlement: when you actually get paid
- Standard: PayFast pays out 2 business days after a payment clears — free.
- Immediate: An immediate payout option settles funds faster for a 0.8% fee on the amount. It's worth using selectively, e.g. only when you urgently need cash for stock, because 0.8% on a R100k month is R800.
- Minimums: Payouts are made to your nominated SA bank account; small balances are swept on schedule depending on your account settings.
Cash-flow tip: If you restock weekly and run on thin margins, the 2-business-day cycle with PayFast means you need working capital cover. The alternative — Peach Payments with near-real-time payouts from early 2026 — is worth comparing if payout speed dominates your decision. Otherwise, the standard PayFast cycle is fine for most stores.
How to reduce your costs
- Shift customers to Instant EFT. It's 2% + min R2 versus 3.2% + R2 for cards — on a R1,000 order that's R22 vs R34. Prompt EFT at the checkout for baskets over ~R500, where EFT approval friction is lower.
- Upgrade from Basic to Grow when volume passes ~R50,000–R100,000/month. The Shopify fee drops from 2% to 1%, saving R1,000/month at R100k revenue — more than the extra subscription.
- Use the R2 minimum intelligently. Instant EFT's min R2 fee hurts on tiny orders, so for low-value digital products, consider whether cards (also min R2) or a different method is cheaper.
- Batch your immediate payouts. Don't use the 0.8% immediate option on every sale; batch it to days you actually need cash.
- Claim your input VAT. Gateway and Shopify fees are typically excluded from VAT, and if you're VAT-registered you can claim input VAT on them at 15% — keep the invoices.
Pros and cons of PayFast on Shopify
Pros:
- Native Shopify app — 15-minute setup, no code
- No monthly fee — free to have the gateway
- Widest local method coverage in one integration (cards, Instant EFT, SnapScan, Zapper, Mobicred)
- Trusted, well-known brand for SA buyers
- Recurring billing for subscriptions
- Card fee dropped to 3.2% in June 2026 after Network International acquisition
Cons:
- Card fee (3.2% + R2) isn't the cheapest — Yoco is 2.95% with no per-txn fee; Paystack is 2.9% + R1
- R2 per-transaction fee hits stores with many small orders hard
- Standard settlement is 2 business days unless you pay 0.8% for immediacy
- Checkout redirects to PayFast's page rather than a fully in-house custom checkout
- No physical card-machine ecosystem (Yoco's advantage)
Troubleshooting common PayFast + Shopify problems
- Orders stuck on "Pending" or unpaid. Usually a webhook/notification mismatch. In the PayFast app, ensure your notify URL and API credentials are saved correctly, and re-save the settings to re-register webhooks.
- Customers say the PayFast page won't load. Check PayFast status (payfast.co.za/status) and confirm your account isn't on hold — an unverified or flagged account blocks checkout.
- Instant EFT fails for a specific bank. Test the affected bank in sandbox; some banks require the customer's app to be updated. Encourage the alternate method.
- Duplicate orders. Order capture mismatches usually come from PayPal-like "abandoned" vs "paid" status confusion — configure your payment status mapping to Paid only on confirmed payment notifications.
- Currency displays in USD in checkout. Set your store currency to ZAR in Shopify Settings → General; PayFast settles in Rands.
- Refunds are slow. Process refunds inside the PayFast dashboard; Shopify doesn't auto-refund through PayFast, so note the manual step for your team.
POPIA and security notes
- You never store card data. PayFast is PCI-DSS Level 1 compliant and card details go straight to PayFast — your POPIA exposure is limited to order and contact data.
- Update your privacy policy. Under POPIA, your Shopify store must disclose what personal information you process (names, email, delivery addresses), why, and your lawful basis. PayFast is a "processor" in POPIA terms; you remain the "responsible party".
- Use 3-D Secure. PayFast's card flow supports 3-D Secure, which reduces chargebacks and fraud — make sure it's enabled in your PayFast settings.
- Secure the admin side. Protect your Shopify admin with strong passwords and two-factor authentication; a hacked admin can redirect payouts.
- VAT-registered? Your PayFast invoices and Shopify fees are input-VAT recoverable at 15% — and if you sell to VAT-registered businesses, include your VAT number on invoices.
PayFast vs the alternatives
| PayFast | Paystack | Yoco | Peach | |
|---|---|---|---|---|
| Card fee | 3.2% + R2 | 2.9% + R1 | 2.95% (no per-txn) | ~2.95% + R1.50 |
| Instant EFT / Pay-by-Bank | 2% + min R2 | 2% EFT | Not offered | Capitec Pay |
| Monthly fee | None | None | None (standard) | None |
| Payout speed | 2 business days | Next business day | Next business day | ~90 seconds |
| Best for | New stores, widest methods | Developers, international | Card-only, in-person too | Volume, recurring |
For a fuller head-to-head, see PayFast vs Paystack and PayFast vs Yoco. And the full seven-gateway landscape is in our Shopify payment gateway alternatives guide and the cluster pillar, the best payment gateway in South Africa.
Beginner Mistakes to Avoid
- Pricing products without stacking Shopify's 2% Basic fee. Your margin dies at 5.4% combined, not 3.2%.
- Forgetting the R2 per-transaction fee. On a R150 order it's 1.3% extra — your real card cost is ~4.5%, not 3.2%.
- Leaving Instant EFT off. You're skipping a method that's cheaper and that a big slice of SA shoppers prefer.
- Not testing the full checkout. You only discover broken payment flows when the first real customer emails you.
- Ignoring settlement timing. If you rely on next-day cash to restock, PayFast's 2-business-day cycle will bite.
- Storing card data yourself. You don't need to and shouldn't — let PayFast handle PCI; you handle POPIA.
- Staying on Basic past R100k/month when Grow's 1% Shopify fee more than pays for itself.
Expert Tips
- Add a small EFT incentive. A 5% discount for Instant EFT often pays for itself: 2% vs 3.2% card fee plus fewer chargebacks.
- Renegotiate at volume. As your PayFast volume grows, ask about custom fee arrangements — large merchants get better than standard rates.
- Map order statuses carefully. Set Shopify to mark orders Paid only on PayFast's "COMPLETE" notification so nothing ships unpaid.
- Monitor your approval rate. A rising decline rate from PayFast means your fraud settings are too aggressive or your checkout UX is failing — check the PayFast dashboard analytics monthly.
- Use the sandbox before launches. PayFast offers a test environment; run a full sandbox order whenever you change themes or add apps.
- Track cost-per-method monthly. Know your split between cards and Instant EFT — it drives both gateway choice and pricing.
The Quick-Start Checklist
- Created and verified a PayFast (Payfast by Network) merchant account
- Collected Merchant ID and Merchant Key from the PayFast dashboard
- Installed the native PayFast app from the Shopify App Store
- Pasted credentials and saved the integration
- Activated desired methods (cards, Instant EFT, SnapScan, Zapper, Mobicred)
- Set store currency to ZAR and mapped payment status to Paid
- Ran test orders on desktop and mobile via card and Instant EFT
- Confirmed 3-D Secure is enabled
- Updated POPIA privacy policy and added VAT number to invoices
- Recalculated product margins with the true stacked cost (gateway + Shopify fee)
South African Case Study
Illustrative example — real-world pattern, not a named client.
The setup: A Durban-based skincare brand on Shopify Basic does R85,000/month across ~280 orders (average order value R304). They've always paid by card at checkout — and never questioned it.
The problem: Payment costs were silently bleeding them. Card fees (3.2% + R2 = ~3.86% at R304 AOV) plus Shopify's 2% Basic fee equalled ~5.86% of revenue, or roughly R4,980 a month just in payment costs.
The fix: With CrazyClicks' guidance, they (1) enabled Instant EFT and added a R25 loyalty credit for EFT payments, and (2) upgraded to the Grow plan once volume justified it. EFT share climbed to ~45% of orders, and Shopify's third-party fee dropped from 2% to 1%.
The result: Combined payment costs fell to ~4.1% of revenue — saving about R1,500 a month (R18,000/year) and improving margin without touching product prices. Customers actually preferred approving a payment in their banking app.
People Also Ask
Q: Does PayFast work with Shopify?
Yes — PayFast has a native app in the Shopify App Store. You install it, enter your Merchant ID and Key, and PayFast's payment methods appear in your Shopify checkout.
Q: Is PayFast now called Payfast by Network?
Yes. Following its acquisition by Network International, PayFast trades as Payfast by Network. Its standard card rate dropped from 3.5% + R2 to 3.2% + R2 on 1 June 2026.
Q: How much does Shopify charge on top of PayFast?
Shopify adds a third-party payment provider fee on every sale because Shopify Payments isn't available in SA: 2% on Basic, 1% on Grow, 0.6% on Advanced.
Q: How long does PayFast take to pay out in South Africa?
Standard settlement is 2 business days, free. An immediate payout option is available for a 0.8% fee.
Q: Can I use PayFast with a Shopify Starter plan?
Yes, PayFast works on Starter, but Starter is limited (no full checkout); most serious stores use Basic or Grow. See how much Shopify costs for plan detail.
Q: Does PayFast support subscriptions on Shopify?
Yes — PayFast supports recurring billing and integrates with Shopify's subscription features.
Q: Is PayFast cheaper than Yoco?
Not for cards. Yoco is 2.95% with no per-transaction fee versus PayFast's 3.2% + R2. But PayFast offers Instant EFT (2% + min R2) and wider methods, and Yoco has no Pay-by-Bank at all.
Frequently Asked Questions
Q: What is PayFast? A: South Africa's most popular payment gateway for small online stores, now branded Payfast by Network. It lets Shopify stores accept cards, Instant EFT, SnapScan, Zapper and Mobicred with no monthly fee.
Q: Is PayFast owned by Network International? A: Yes. Network International acquired PayFast, and it now operates as Payfast by Network. The card fee dropped to 3.2% from 1 June 2026.
Q: How much does PayFast charge? A: 3.2% + R2 per card transaction, 2% + min R2 for Instant EFT/Capitec Pay, supported methods at PayFast's standard fee structure, and no monthly fee. Figures are mid-2026 and exclude VAT.
Q: Can I use PayFast with Shopify? A: Yes — native app, 15-minute setup, no developer required.
Q: What are the total fees on Shopify Basic with PayFast? A: ~5.2–5.5% combined for card (3.2% + R2 PayFast + 2% Shopify) and ~4.0% for Instant EFT.
Q: How fast does PayFast pay out? A: 2 business days standard, or immediately for a 0.8% fee on the amount.
Q: Does PayFast charge a monthly fee? A: No. No subscription on the standard account; you pay only per transaction.
Q: Is PayFast safe and POPIA compliant? A: PayFast is PCI-DSS compliant and card data never touches your server. You remain responsible under POPIA for the order data you collect, and need a proper privacy policy.
Q: How do I get paid faster with PayFast? A: Use the immediate payout option (0.8% fee) or, better, pair PayFast with a gateway offering faster standard settlement (e.g. Peach) for cash-flow-critical periods.
Q: Can I use more than one gateway with PayFast on Shopify? A: Yes — many stores run PayFast alongside Ozow (for Pay-by-Bank) or Paystack (for international cards).
Summary
PayFast is the easiest, most popular way for South African stores to get paid on Shopify: native integration, no monthly fee, widest local payment coverage, and now a lower 3.2% + R2 card rate under its new Network International ownership. The catch is the stacked cost — Shopify's 2% Basic third-party fee makes a card sale cost ~5.2–5.5% in total. Budget honestly, push Instant EFT, upgrade plans at the right volume, and PayFast remains a superb default for new and small stores.
Key Takeaways
- PayFast is now Payfast by Network; card fee is 3.2% + R2 (down from 3.5% on 1 June 2026), Instant EFT 2% + min R2, no monthly fee.
- Shopify stacks a 2%/1%/0.6% third-party fee on top of PayFast — a Basic card sale really costs ~5.2–5.5%.
- Native Shopify app: install, paste credentials, activate methods — no developer needed.
- Standard settlement is 2 business days; immediate payout costs 0.8%.
- Shifting customers to Instant EFT and upgrading to Grow at the right volume are the two biggest cost levers.
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