Shopify

Shopify Yoco: Online Payments & Card Machines in SA (2026)

Alister

E-commerce Consultant

| 6 Aug 2026 17 min

Introduction

You've built your Shopify store. You've got stock, photos and a checkout that works. Then you hit the one wall every South African Shopify merchant runs into: Shopify Payments isn't available in this country, so you need a local payment gateway to actually get paid. At the same time, if you run a cafe, a clothing store or any business with a physical counter, you probably also want to take cards in person with a card machine. Yoco, the Cape Town fintech, is one of the most popular answers to both problems — but "popular" isn't the same as "best for your numbers."

This guide breaks down exactly how Yoco works with Shopify: the real fees in Rands, the true total cost once Shopify's own fees are stacked on top, how to integrate the two in under an hour, and an honest comparison with PayFast and Peach so you can decide with your eyes open.

Quick answer: Yoco works with Shopify through its online payment gateway, which you install from the Shopify App Store. Yoco charges 2.95% per local card transaction and 3.40% on international cards, with no per-transaction fee. On top of that, Shopify adds its third-party payment provider fee because Shopify Payments isn't available in South Africa: 2.0% on Basic, 1.0% on Grow and 0.6% on Advanced. A typical Basic-plan store ends up paying around 4.9% of every local card payment (Shopify 2% + Yoco 2.95%). Yoco's card machines are standalone terminals — they don't pair natively with Shopify POS, so in-person and online payments need light manual reconciliation. Yoco's Plus/Pro online plans at R249/R499 a month can lower the gateway rate to as low as 2.55%. For omni-channel sellers and cafes, Shopify + Yoco is a practical, solid combination.

Need help weighing up gateways or building your store? Get expert help from CrazyClicks — we're a full-service digital agency in Cape Town.

Why this matters for South African businesses

South Africa has a genuinely unusual e-commerce payments landscape, and it shapes this decision more than any feature comparison.

Shopify Payments doesn't exist here. As of mid-2026, Shopify still doesn't offer its own gateway to South African merchants, so every single SA store pays Shopify's "third-party payment provider" fee on top of its monthly plan. There's no way around it.
There are over 22,000 active South African Shopify stores as of May 2026, growing roughly 28% year-on-year. That means thousands of local business owners are making exactly this decision right now.
Card culture is strong. South Africans pay by card at the till and online far more than they used to. A store that can't take cards quietly loses sales.
The choice is a maths problem, not a brand loyalty problem. At 2.95% vs 3.2% + R2, Yoco vs PayFast looks like a rounding difference — but multiply it by R100,000 of monthly sales and it's R2,400+ a year, before you even count the R2 per-transaction fee.
POPIA compliance applies to your gateway too. Whoever you choose handles your customers' card data, so the gateway's security and your privacy policy matter — not just its fee card.

Key fact: Because Shopify Payments is unavailable in South Africa, Shopify charges an extra third-party payment provider fee on every sale: 2.0% on Basic, 1.0% on Grow, 0.6% on Advanced and 0.2% on Plus (Shopify, 2026).

If you haven't decided Shopify is right for you yet, our Shopify vs WooCommerce showdown and Shopify pricing guide are worth a read first. This article assumes you've chosen Shopify and are now picking your payments.

What is Yoco?

Yoco is a South African fintech company founded in Cape Town in 2015. It built its name selling small, affordable card machines to merchants who were previously told they were too small for card acceptance — think food trucks, market stalls, township spaza shops and coffee shops. Today it has grown into a broad SME financial services brand offering:

Card machines (POS terminals): the Yoco Go and Yoco Neo, used for in-person, card-present payments with tap, chip and PIN.
The Yoco Business app: the dashboard where you track sales, see payouts, send invoices and manage your till.
Online payments gateway: lets you take card payments on websites and online stores — which is what plugs into Shopify.
Additional SME tools: business banking-adjacent services, cash advances and business insights.

For a South African retailer, Yoco's appeal is that one brand covers both worlds: card payments at the counter and card payments online. There aren't many local providers that do both on one dashboard.

Key fact: Yoco's online payment gateway integrates with Shopify through the Shopify App Store. Its card machines are separate, standalone devices that run on the Yoco app — they do not connect natively to Shopify POS (Yoco, 2026).

Yoco's fees explained

Yoco's pricing is simple at the standard level, with optional monthly plans that lower your rate. Figures below are mid-2026, ex-VAT, as published by Yoco.

Fee item	Standard rate	With Plus plan (R249/mo)	With Pro plan (R499/mo)
Local card transactions	2.95%	As low as 2.55%	As low as 2.55%
International cards	3.40%	Lower rate tier	Lower rate tier
Per-transaction fee	None	None	None
Monthly fee	R0	R249	R499

What the fine print means:

Local cards = 2.95%. This applies to Visa, Mastercard and Amex issued in South Africa, charged on the full order value including VAT and delivery.
International cards = 3.40%. Any foreign-issued card — including cards used by overseas tourists or international customers — costs the higher rate.
No per-transaction fee. Unlike PayFast (3.2% + R2) or Paystack (2.9% + R1), Yoco doesn't add a fixed charge per sale. On a R450 average order, that R2 difference adds up to about 0.4% in effective fees — enough to flip a comparison.
Plus and Pro plans (R249/R499 per month) are aimed at higher-volume merchants. If you're doing enough turnover, the lower rate more than pays for the monthly fee. As a rule of thumb: the plans start to justify themselves once you process around R60,000-R100,000 a month in cards.
Refunds and chargebacks: refunds usually carry a small processing fee, and chargebacks come with admin fees — standard industry behaviour, so budget for them.

Worked example: Yoco fees on a real store

Let's say you run a Johannesburg online clothing store doing R80,000 a month in card payments, average order R500, on Yoco's standard rate:

Item	Calculation	Amount
Local card volume	95% of R80,000	R76,000
Local card fees	2.95% of R76,000	R2,242
International card volume	5% of R80,000	R4,000
International fees	3.40% of R4,000	R136
Total Yoco fees		~R2,378/month

Now add a R249 Plus plan (rate drops to 2.55%):

Item	Calculation	Amount
Local card fees	2.55% of R76,000	R1,938
International fees	~3.00% of R4,000	R120
Plus plan		R249
Total		~R2,307/month

The Plus plan saves you roughly R70 a month at this volume — barely a wash. At R150,000/month the saving grows to several hundred Rands, which is when the plan starts to make real sense. Do the maths on your own volume, not on the headline rate.

How Shopify's fees stack on top

This is the part most blogs skip, and it's the part that decides whether Yoco is actually cheap for you.

Because Shopify Payments is unavailable in South Africa, every payment you take via Yoco triggers two sets of fees: Yoco's gateway fee plus Shopify's third-party payment provider fee.

Shopify plan	Monthly cost (approx)	Shopify third-party fee	Yoco card rate	Total per local card sale
Starter	~R90	Not applicable	2.95%	~4.95% (Yoco only, no Shopify fee on Starter checkout)
Basic	~R450	2.0%	2.95%	~4.95%
Grow	~R1,170	1.0%	2.95%	~3.95%
Advanced	~R7,200	0.6%	2.95%	~3.55%
Plus	from ~R41,000	0.2%	2.95%	~3.15%

With a Yoco Plus/Pro plan (rate 2.55%):

Shopify plan	Shopify third-party fee	Yoco rate	Total per local card sale
Basic	2.0%	2.55%	~4.55%
Grow	1.0%	2.55%	~3.55%
Advanced	0.6%	2.55%	~3.15%

The full stacked cost on a Basic store

Take the realistic case from the facts: a typical Basic-plan store doing R100,000/month in sales on about 250 orders:

Cost item	Calculation	Monthly amount
Shopify Basic subscription	~R450-R730 (incl. app fees)	~R450
Shopify third-party fee	2% of R100,000	~R2,000
Yoco gateway fee	2.95% of R100,000 (local)	~R2,950
3-4 essential apps		~R700-R1,400
Domain		~R15-R150
Total platform + payment cost		~R6,100-R8,950/month

That's roughly 6-8% of revenue before you spend a cent on marketing. This is the real number you're signing up for, and it's why payment gateway choice matters so much in South Africa.

Key fact: Combined with Shopify, Yoco's per-sale cost lands at roughly 4.95% on a Basic plan, 3.95% on Grow and 3.55% on Advanced for local card payments (CrazyClicks calculation from Shopify and Yoco published rates, 2026).

Step-by-step: connect Yoco to your Shopify store

The integration is an official Shopify app, so it's a straightforward setup — most merchants are live in under an hour.

Step 1: Create (or confirm) your Yoco business account

Go to yoco.com and sign up with your South African business details. You'll need:

Your registered business name and ID/turnover documentation
A South African business or personal bank account for payouts
Proof of address, depending on your account type

If you already use a Yoco card machine, use the same account so your online and in-person money lands in one dashboard.

Step 2: Install the Yoco app from the Shopify App Store

In your Shopify admin, go to Apps > Shopify App Store, search for "Yoco", and open the Yoco Online Payments app. Click Add app and approve the permissions it requests.

Step 3: Connect your Yoco account

Follow the prompts to log into your Yoco account and authorise the connection. Shopify and Yoco will now be linked, and your Yoco payment methods (card) will become available at checkout.

Step 4: Activate Yoco as your checkout provider

In Shopify admin, go to Settings > Payments, find Yoco in your payment providers, and set it as active. Make sure it's above or exclusive of any other gateway you may have tried, so it appears at checkout.

Step 5: Set your currency and check international cards

Your store should be priced in ZAR — Shopify fully supports Rand storefronts. Decide whether you want to accept international cards (rate 3.40%) and enable/disable accordingly. If you sell mostly to locals, leaving it on is harmless; if you get chargebacks from abroad, switch it off.

Step 6: Run a test transaction

Place a test order or use Yoco's test mode to confirm the flow works: the customer sees a Yoco checkout page, the payment is authorised, the order appears in Shopify as paid, and stock decrements correctly.

Step 7: Mark in-person card sales as paid (if you use a Yoco machine)

For every sale taken on your Yoco card machine, open the matching order in Shopify and mark it paid manually. There's no automatic link between the machine and Shopify POS, so build a small end-of-day ritual — this is the one genuinely fiddly part of the setup.

Yoco card machines and Shopify POS

This is where a lot of South African retailers get confused, so let's be crystal clear.

Shopify POS (the app that turns a phone or tablet into a till, synced with your online store) only pairs natively with Shopify's own card readers. And as of 2026, Shopify does not officially sell or support its card readers in South Africa. That means:

You can't plug a Yoco machine into Shopify POS and have it "just work" like a Shopify reader does in the US.
Instead, you run Shopify POS for the catalogue, inventory, receipts and order sync, and take the actual card payment on your Yoco machine as a standalone device.
After each sale you mark the Shopify order as paid. It's manual, but it's reliable and plenty of SA retailers do exactly this.

Two honest options in-store:

Approach	What it is	Best for
Yoco machine + Shopify POS, manual reconciliation	Take cards on Yoco, track catalogue/inventory on Shopify POS, mark orders paid	Retailers who want one inventory system and don't mind a light manual step
Yoco machine + Yoco app only	Keep Shopify purely for the online store; run the shop floor on Yoco	Cafes and quick-service counters where inventory sync matters less

Key fact: Shopify's own card readers are not officially available in South Africa, so SA retailers pair Shopify POS with standalone local terminals like Yoco and reconcile manually (Shopify, 2026).

For a full walkthrough of your in-store options, see our dedicated guide to Shopify POS in South Africa.

Settlement and payouts

Knowing when money lands in your bank account is half of cash flow planning.

Card machine transactions settle to your South African bank account typically within one to two business days, once payouts are activated. Yoco supports payouts to major SA banks including Capitec, Standard Bank, FNB and Absa.
Online gateway payouts follow your Yoco plan's settlement schedule — commonly daily or next business day depending on your volume and tenure.
Weekends and public holidays delay settlement, so plan payroll and supplier payments around long weekends like Easter.
You can track every payout in the Yoco Business app, and reconciliations export cleanly to your accounting system.

Yoco vs PayFast vs Peach: honest comparison

All three are official Shopify-compatible options for South African merchants, and all three coexist with Shopify's third-party fee. The real differences are in pricing model, payment methods and payouts.

Feature	Yoco	PayFast	Peach Payments
Local card rate	2.95%	3.2% + R2	~2.95%
International card rate	3.40%	Higher (list pricing)	~3.50%
Per-transaction fee	None	R2	R1.50
Pay-by-Bank / Instant EFT	Not offered	2.0% + R2 (Instant EFT, Capitec Pay)	Capitec Pay supported
Monthly fee	R0 (or R249/R499 for lower rates)	None	None
Card machines	Yes (Yoco Go/Neo)	No	No
Payouts	1-2 business days	Standard schedule	Real-time (~90 sec) from early 2026
Recurring billing	Limited	Yes	Yes
Best for	Omni-channel, cafes, in-person + online	Shoppers who love Pay-by-Bank / EFT	Higher volume, recurring revenue

How to choose

Choose Yoco if you have a physical counter and a Shopify store, you want one dashboard for both, and your customers mostly pay by card. The lack of a per-transaction fee favours you on low-value, high-frequency sales.
Choose PayFast if your customers strongly prefer Pay-by-Bank / Instant EFT (common for furniture, car parts and B2B buyers), or you want the widest local method coverage. PayFast's card rate is higher, so card-heavy stores pay more.
Choose Peach if you're doing higher volume, need recurring billing, or cash flow is so tight that real-time payouts are worth it. Peach's rate is competitive with Yoco's, though it doesn't sell card machines.

For deeper head-to-heads, read our PayFast vs Yoco and best payment gateway for South Africa guides.

Pros and cons

Pros of Shopify + Yoco:

One provider for online and in-person. Fewer logins, one dashboard, one set of statements.
Lowest per-sale card cost at the standard tier. 2.95% with no per-transaction fee beats PayFast's 3.2% + R2 and Paystack's 2.9% + R1 on low-value orders.
Trusted local brand. Cape Town-born, widely used by SA SMEs, with local support.
Fast, simple Shopify setup. The official app installs in minutes with no code.
Yoco machines are cheap to rent or buy and easy to move between counters, markets and pop-ups.
No monthly fee at standard rates. Ideal for small or seasonal stores.

Cons of Shopify + Yoco:

No Pay-by-Bank / EFT. If your customers prefer EFT, Yoco simply won't help you there.
Manual reconciliation with Shopify POS. No native machine-to-POS link means a daily manual step.
International cards cost 3.40%. Cross-border sales get pricier, and Yoco's international coverage is thinner than global-first gateways.
Lower-rate plans only pay off at volume. The R249/R499 plans need roughly R60,000-R100,000 a month in cards to justify themselves.
You still pay Shopify's 2%/1%/0.6% fee. Yoco can't remove that; no SA gateway can.

Who is Shopify + Yoco best for?

Use this as a rough decision tree:

Cafe, coffee shop or quick-service counter that also sells online? Yoco is a natural fit. Take cards at the till, take orders online, track everything in one app.
Retail shop with a website, two counters and a stockroom? Yoco + Shopify POS (with manual card reconciliation) gives you one inventory system across both channels.
Market stall / pop-up / township retailer testing a Shopify store? Yoco's cheap machines and no-monthly-fee gateway keep your risk low.
B2B wholesaler whose customers pay by EFT? Don't pick Yoco. Look at PayFast or Ozow's Pay-by-Bank.
Subscription business with recurring billing? Peach is the stronger pick.
High-volume store pushing R250,000+ a month? Negotiate directly with Peach or a provider like PayGate (DPO) — the maths changes at that scale.

Beginner mistakes to avoid

Ignoring the stacked cost. Yoco at 2.95% plus Shopify's 2% on Basic means ~4.95% of every sale. Budget for the total, not just the gateway rate.
Turning on international cards without checking the rate. A holiday surge of foreign tourists is great — at 3.40% per card. Price your shipping and margins accordingly.
Skipping the test transaction. A broken checkout loses customers silently. Always test before launch.
Forgetting to mark Yoco machine sales as paid. Your inventory and cash flow will drift if you don't reconcile in-store card sales with Shopify orders.
Buying the Plus/Pro plan on a low-volume store. At R50,000/month the plan can cost you more than it saves. Do the maths first.
Not budgeting for chargeback and refund fees. They're small but real, and they eat into months where refunds spike (think January after festive returns).
Staying on Yoco without rechecking rates. Fees move. Every 12 months, re-run the Yoco vs PayFast vs Peach maths on your actual volume.
Treating POPIA as an afterthought. Your gateway holds customer card data; make sure your privacy policy and data handling comply before you take live orders.

Expert tips

Turn your sale size into a rate. Divide the R2 per-transaction fee your alternatives charge by your average order value to get a "rate-equivalent." A R2 fee on a R100 order is effectively 2% extra — Yoco's no-fee model wins there.
Use Shopify's manual payment method for Yoco-machine sales. Create a "Paid via Yoco terminal" payment method in Shopify so orders are marked with a traceable label, not a vague "cash."
Reconcile daily, not monthly. Ten minutes at closing time beats a three-hour spreadsheet session in March.
Ask Yoco about volume-based rates. High-volume merchants often get custom pricing that isn't published — but you have to ask.
Watch the festive season. Black Friday through January can be 40%+ of annual card volume. Confirm your Yoco plan handles the spike and that your Plus/Pro upgrade would be worthwhile across those months.
Use the same Yoco account for machine and gateway. You get consolidated statements, simpler tax prep and better settlement history.
Price in Rands, but plan for forex. If you sell to customers abroad, build the 3.40% into your international pricing strategy.
Claim your VAT input credits. Yoco and Shopify fees are typically ex-VAT; if you're VAT-registered, claim the input VAT on both.

The quick-start checklist

Created your Yoco business account with KYC and a SA bank account
Decided standard vs Plus/Pro plan based on your monthly card volume
Installed the Yoco app from the Shopify App Store
Connected and activated Yoco as the checkout provider
Confirmed store currency is ZAR
Decided on international card acceptance (3.40%)
Ran a live test transaction
Set up a daily reconciliation habit for Yoco machine sales
Updated your privacy policy for POPIA compliance
Budgeted the full stacked cost (Shopify fee + Yoco fee) into pricing
Booked 15 minutes in your diary to re-check rates in 12 months

South African case study

Illustrative example, not a real client.

The business: Urban Bean, a specialty coffee roastery with one cafe in Cape Town's Woodstock and a Shopify store selling beans and brewing gear nationwide.

The setup: The cafe takes walk-in card payments on two Yoco Neo machines. The online store runs Shopify on a Grow plan (~R1,170/month) with Yoco as its gateway. Both use the same Yoco account.

The numbers: In-store card sales average R95,000/month; online sales average R45,000/month. The owner signed up for Yoco's Pro plan (R499/month) because combined card volume is around R140,000/month.

Item	Monthly amount
In-store Yoco fees (~2.55% on R95,000)	~R2,423
Online Yoco fees (~2.55% on R45,000)	~R1,148
Shopify Grow plan	~R1,170
Shopify third-party fee (1% on R45,000)	~R450
Yoco Pro plan	~R499
Total	~R5,690/month

The trade-off: At checkout, Urban Bean also offers EFT via a PayFast link for its few wholesale customers — the owner accepts that Yoco can't do Pay-by-Bank. The owner estimates the single-dashboard approach saves about four hours of admin a week versus juggling separate machines and gateways. The 4.3% effective cost of online sales (1% Shopify + 2.55% Yoco + 0.55% in card scheme extras) is budgeted into pricing, and beans stay competitive.

What worked: one dashboard for in-store and online money; clean end-of-day reconciliation; VAT input claims on both Shopify and Yoco fees.

Frequently Asked Questions

Q: Is Shopify Payments available with Yoco in South Africa? A: No. Shopify Payments is not available to South African merchants at all, so you must use a third-party gateway. Yoco is one of several options, and you'll still pay Shopify's third-party fee (2.0% on Basic, 1.0% on Grow, 0.6% on Advanced) on every sale.

Q: What are the total fees for Shopify with Yoco on a Basic plan? A: Around 4.95% per local card sale: Yoco's 2.95% plus Shopify's 2.0% third-party fee. With a Yoco Plus/Pro plan the rate can drop to about 4.55%. Add your subscription, apps and domain on top for the true monthly cost.

Q: Does Yoco support recurring subscriptions on Shopify? A: Yoco's online gateway is primarily built for one-off card payments. If you're selling subscriptions, Peach Payments' recurring billing is the stronger choice.

Q: How long does it take to set up Yoco with Shopify? A: About 30-60 minutes including KYC, if your business documents are ready. The app installs quickly; most of the time goes into Yoco's account verification.

Q: Can I use Yoco and PayFast on the same Shopify store? A: Yes. Shopify lets you activate multiple payment gateways, so you could offer Yoco for card payments and PayFast for Pay-by-Bank/EFT at the same checkout.

Q: Does Yoco charge for refunds? A: Refunds generally carry a small processing fee and chargebacks carry admin fees. Always read Yoco's current fee schedule and budget for return-heavy months.

Q: Is Yoco safe to use with Shopify? A: Yes. Yoco is an established, regulated South African payments provider, and its gateway is a verified Shopify app. Your store still needs a POPIA-compliant privacy policy because the gateway processes customer card data.

Q: What happens to my Yoco money over weekends? A: Payouts typically pause over weekends and public holidays, so money taken on a Friday afternoon usually lands the following business day. Plan supplier payments around long weekends.

Q: Can a township business or informal trader use Yoco with Shopify? A: Yes. Yoco was built for small merchants, and its no-monthly-fee gateway plus affordable machines make it accessible. You'll need the standard KYC documents and a South African bank account for payouts.

Q: Does Yoco work with Shopify's POS Lite or POS Pro plans? A: The Yoco online gateway works with any Shopify plan. But because Yoco machines don't pair natively with Shopify POS, in-store card payments are taken on the machine itself and reconciled manually — this applies regardless of your POS tier.

Summary

Yoco is a strong, honest choice for South African Shopify merchants who take cards online and in person. At 2.95% with no per-transaction fee, it's the cheapest card-only option of the major local gateways, and one account covers your machine and your checkout. The two real caveats are the stacked Shopify fee (which every SA gateway carries) and the manual reconciliation required between Yoco machines and Shopify POS. Do the maths on your own volume before choosing a paid plan, and remember the gateway is only one line in a store budget that typically runs 6-8% of revenue on Shopify.

Key Takeaways

Yoco charges 2.95% local / 3.40% international, no per-transaction fee; Plus/Pro plans (R249/R499 per month) lower the rate to as low as 2.55%.
With Shopify's third-party fee added, expect roughly 4.95% on Basic, 3.95% on Grow and 3.55% on Advanced per local card sale.
Shopify Payments isn't available in South Africa, so the third-party fee is unavoidable — no SA gateway escapes it.
Yoco card machines don't sync natively with Shopify POS; you'll reconcile in-person sales manually.
Yoco wins on card payments and omni-channel simplicity; PayFast wins on Pay-by-Bank/EFT; Peach wins on real-time payouts and recurring billing.

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