Shopify Payments is not available to South African stores. That matters for cost, not just convenience: when you connect a third-party gateway instead, Shopify charges its own additional transaction fee on every order, on top of whatever the gateway takes. Two lines on two invoices, easy to under-count, and together they push real processing cost on Shopify to roughly 4% to 5%.
How big is the Shopify surcharge?
It depends only on your Shopify plan, read off Shopify’s own pricing
page Third-party payment provider fees by plan Read off the provider's own published pricing page. Checked this month, on 20 Jul 2026.
| Plan | Monthly price | Fee on third-party gateway orders |
|---|---|---|
| Basic | $19 (billed yearly) · $25 monthly | 2.0% |
| Grow | $49 · $65 | 1.0% |
| Advanced | $299 · $399 | 0.6% |
| Plus | From $2,300 | 0.2% |
Shopify bills in US dollars and the fee applies because Shopify Payments is unavailable here, so every SA store pays it. It is charged per order whichever local gateway you connect, cards and instant EFT alike.
Note what this fee is not: it is not a payment-processing fee. Shopify moves no money on these orders. It is a platform surcharge for not using the in-house processor that South Africans are not allowed to use, which is why it stings, and why it belongs in your maths anyway.
What does a card sale on Shopify really cost?
Stack the two lines. Take Paystack’s local card rate of 2.9% + R1, which on a R650 basket works out to an effective 3.05% before VAT, then add your plan’s surcharge:
Gateway side ex VAT, computed at a R650 basket; your own basket moves it. Swap in any provider’s effective rate from the calculator, then add your plan’s percentage.
Run the same stack with your numbers: work out your gateway’s effective rate at your basket size, then add your plan’s row from the table. That final number is what a card sale on Shopify in South Africa actually costs, and it is the number to use when you set prices and margins.
Should you upgrade the plan or switch the gateway?
Both levers move the same total, so compare them honestly, in dollars, because that is how Shopify bills:
- Basic to Grow drops the surcharge by a full 1% and costs about $30 more a month on yearly billing. It pays for itself once you process about $3,000 a month through checkout. Most stores past hobby volume clear that easily.
- Grow to Advanced drops it a further 0.4% for about $250 more a month, which needs around $62,500 a month in sales before the fee saving covers the plan. That is a real store, not a side project.
Meanwhile a gateway switch is free. The spread between local gateways’ effective rates can exceed a percentage point at some basket sizes, which is the same order of magnitude as a plan upgrade, without the monthly commitment. Exhaust the gateway lever first, then let volume justify the plan.
How do you keep the total down?
- Pick the gateway on effective rate, not headline. The comparison shows every local option Shopify supports; the calculator ranks them at your basket and volume.
- Offer instant EFT alongside cards. The bank rails are cheaper on the gateway side, as covered in instant EFT vs cards. Shopify’s surcharge still applies, but the gateway line shrinks.
- Re-check the plan tier once a quarter. The breakevens above are just arithmetic; your volume decides them, and it changes.
- Price it in. If your margin model says “card fees”, make the line read “card fees plus Shopify surcharge”. The stores that get surprised are the ones that budgeted the gateway rate alone.
None of this makes Shopify a bad platform for South Africans; it makes it a platform with a known extra line item. Know the line, add it to the maths, and decide with the true number on the table.
