How to Connect Yoco to Shopify: Setup, Fees and Going Live

How Yoco Connects to Shopify

Shopify Payments is open only to businesses in the countries on Shopify's supported-countries list, and South Africa isn't one of them. A South African store therefore takes cards through a third-party payment provider, and Yoco is one: it publishes the Yoco Payments app on the Shopify App Store, free to install, with app support provided by Yoco.

Two Shopify rules shape the setup. Only the store owner can add a payment provider, and you can have only one credit card payment provider activated at a time, so Yoco becomes the one that takes your cards. The work is split between Yoco's side and Shopify's:

The part merchants expect to be hard, copying keys between two dashboards, isn't there. Yoco's Shopify help article puts it plainly:

This guide covers Yoco alone. If you're still choosing a provider, see which other payment providers a South African store can connect.

If Payfast is the other provider on your list, our Payfast guide covers its setup, fees and fixes.

What You Need Before You Connect Yoco

Yoco's developer guide is blunt about the first item: to receive payments, a Yoco profile is mandatory. The rest of the list follows from how Yoco approves online selling.

Hardware isn't one of them. Asked whether you need a card machine for its online products, Yoco answers “No. All three options work without one”; the R199 sign-up fee in Yoco's plans and fees is what you pay instead of owning one.

Verification is the step that decides when you can sell. For its Payment Gateway, Yoco says it also verifies your website, and the gate is simple:

Yoco's domain-verification guide adds that the website must be finished and live: a domain is automatically rejected if the site is password-protected or still showing a “coming soon” page, so take your storefront off Shopify's password page before you install the app. For Shopify, Yoco says installing the plugin adds your store's domain and submits it for review automatically, and the domain check only takes a few minutes once your site is reachable. Passing verification doesn't by itself put Yoco on your checkout; the checkout-side checks are separate.

How to Connect Yoco to Shopify, Step by Step

Yoco's route starts on its side. Yoco's Shopify help article, updated July 17, 2026, sends you from the Yoco Web App to the Shopify App Store through a How to Connect button, which lands on the Yoco Payments listing. That listing is step 3 of the checklist below.

Shopify App Store listing for Yoco Payments

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The checklist follows the order in Yoco's help article and developer guide. Tick each step as you finish it; you'll move between the Yoco Web App, the App Store and your Shopify admin.

Yoco's developer guide words step 4 from the app's side: the Shopify application automatically attempts to connect to your Yoco account. Yoco's two pages name the final button differently, Activate Yoco in the help article and Activate in the developer guide, so look for either.

Yoco also published a 46-second walkthrough of the setup on its own channel in June 2022. Screens may have changed since; the checklist above follows Yoco's current help article.

Test Mode and Going Live

Yoco documents testing in two places. Its developer testing guide has you tick Test mode in Yoco's settings, pay with the test card details from the Yoco App and then confirm the order in Shopify and the payment under Sales history in the Yoco App. Yoco's help article asks you to run a test payment of at least R2.00 and check that the correct business name shows on the Yoco checkout page. That help article doesn't mention Test mode, so it doesn't say whether that payment is made in Test mode or live.

The developer guide is clear that the test is optional, and just as clear that you should run it:

Going live is the same screen in reverse. Yoco's going-live guide has you go to Settings > Payments, select Manage next to Yoco Payments, clear the Test mode checkbox and select Save.

Which Payment Methods Yoco Adds to Your Checkout

Four Yoco pages describe what shoppers can pay with, and they don't list quite the same cards:

Yoco's fee table does price an Amex line, but that page covers all of Yoco's online products, not the Shopify app alone.

Yoco's Gateway help article, which names Shopify among its platforms, lists international and local Amex among the cards Yoco Gateway accepts. It also says Yoco Gateway doesn't currently support subscriptions or recurring billing.

What Yoco on Shopify Costs

The app itself costs nothing: the listing reads “Free to install. Additional charges may apply.” The charges come on two separate bills. Yoco's help puts it in one line, that Shopify fees are independent of Yoco transaction fees, so you budget for both.

Yoco's Online Rates by Plan

Yoco has three plans, Core, Plus and Pro, and its online rate depends on both the plan and your sales volume:

Which column you're in depends on volume, by Yoco's rule: if your average monthly sales over the last three months are below R50,000, you pay the rate in the first local card column, and once your rolling three-month average reaches R50,000 or more, your local card rate drops automatically. Yoco's online-payments page adds that online and card machine sales count towards the same monthly turnover, which can lower the rate on both. Yoco charges 15% VAT on its transaction fees, as the law requires.

Two more points sit outside the table. Yoco's plans and fees article says merchants who don't take payments on a Yoco card machine pay a once-off, non-refundable R199 sign-up fee. Yoco's Shopify help article, by contrast, says Yoco for Shopify comes with “no long-term contracts or setup fees”; the two pages, both read November 10, 2026, don't reconcile the difference.

Yoco's online-payments page adds that if you sign up without buying a card machine, a once-off signup fee is paid at checkout, so the sign-up checkout is where you'll see whether it applies. And Yoco's online-payments page says there's no monthly fee for any of its online options without mentioning plan subscriptions; its plans and fees article lists Plus at R249 and Pro at R499 per month per location.

Shopify's Third-Party Fee on Top

Shopify charges its fee on all transactions processed through third-party payment gateways. Its pricing page lists the rate at 2% on Basic, falling to 1% on Grow, 0.6% on Advanced and 0.2% on Plus. For your location, Shopify's third-party providers page says to check the pricing page or contact Shopify Support.

Shopify's billing help is explicit that this fee doesn't replace Yoco's:

Take one R2,000 order paid with a local card on Yoco's Core plan, below the R50,000 volume line. Yoco's fee is R61.00 ex VAT (R70.15 with 15% VAT). Shopify, for its part, charges stores located in South Africa 15% VAT on eligible Shopify billing charges. Here is what the two fees add up to on each Shopify plan, before VAT:

Yoco's Core rate for a local card below R50,000 plus Shopify's third-party transaction fee by plan, both before VAT, as of November 10, 2026.

The two parts move independently: Shopify's part is set by your Shopify plan, while Yoco's depends on your Yoco plan and your sales volume.

Whether that justifies a plan upgrade depends on your volume; our gateway guide works through how the surcharge is built.

Refunds and Payouts

After launch, the money side of a Yoco order lives mostly in Yoco. Yoco's listing points you to detailed sales and payout reporting in the Yoco App and Web App, while Shopify keeps the order and bills its own fee.

Where to Refund a Yoco Payment

Yoco's Shopify help article says all transactions appear in the Yoco App, mobile or web, where you can manage refunds and view payouts. Yoco's refund guide says debit card payments can only be refunded on the same day as the original payment, and that refunds in the Yoco App only go through if your Yoco balance, your pending payout, covers them.

Shopify's rule runs the other way. In a country where Shopify Payments isn't available, an order refunded from Shopify admin gets its transaction fees refunded in proportion to the amount refunded, while card fees are set and charged by the gateway.

Yoco's refund guide lists a second route: partial refunds can also be issued from the Shopify Admin portal, by opening the order in Orders, selecting Refund, entering the amount or items and a reason, and selecting Refund again. What the Yoco and Shopify pages we read on November 10, 2026 don't say is whether a refund made in the Yoco App shows on the Shopify order, so check both the Shopify order and the transaction in the Yoco App after your first refund.

For the fee side in more detail, see what happens to Shopify's transaction fee on a third-party gateway refund.

When Yoco Pays You

Yoco says your payout reflects in your account after 1–2 business days, depending on your bank, and online payments follow your usual Yoco payout schedule, together with in-person sales. Yoco lists four ways to get paid:

• Standard — 1–2 business days, depending on your bank.
• Weekly — free for all plans.
• Fast — free on the Pro plan.
• Instant — the fourth option Yoco lists.

One detail differs between Yoco's own pages: its payouts article gives a minimum payout of R10, while its plans and fees article gives R50. Neither says which governs, so if a small balance hasn't arrived, look at the payout reporting in the Yoco App or Web App before you assume a fault.

When Yoco Doesn't Show at Checkout or Isn't Switched On

Most problems trace back to one of the two checks, Yoco's verification or the settings on Shopify's Payments page. Shopify's general route for a third-party provider, when Shopify Payments isn't available, is Choose a provider in Settings > Payments, and that list is filtered by your store address; Yoco's own route is the App Store listing.

For anything else, the listing says app support is provided by Yoco. And if you ever need to switch Yoco off, Yoco's help article puts an Uninstall Yoco button at the bottom of the Yoco screen in Settings > Payments.

The Bottom Line

The setup itself is short. What can hold up your launch is Yoco's verification, and what costs money is the pair of fees on every order.

Frequently Asked Questions