If you are setting up a Shopify store in Nigeria, the first surprise usually comes at checkout. Shopify’s own payment system, Shopify Payments, is not available to stores in Nigeria. That does not mean you cannot sell. It means you connect a third-party payment provider, and how you set it up decides whether customers can actually pay you in naira.
The Short Answer: Use Paystack or Flutterwave
Paystack is available on Shopify as a third-party payment provider for merchants in Nigeria, and Flutterwave offers a Shopify app too. Many Nigerian merchants start with Paystack for domestic naira payments, and look at Flutterwave when they need wider African coverage or mobile money.
How Checkout Works With Paystack
When a customer chooses Paystack at checkout, Shopify sends them to Paystack’s secure payment page. They pay there and are returned to your store, and Shopify records the order. The payment options the customer sees, such as card, bank transfer or USSD, are controlled by your Paystack account rather than by Shopify, so make sure the channels you want are switched on in Paystack.
Set It Up Step by Step
- In your Shopify admin, open Settings, then Payments.
- Choose to add a payment method and search by provider for Paystack (or Flutterwave).
- Activate it and connect your Paystack account.
- Set your store currency to naira (NGN) and list your products in naira.
- Place a test order in Paystack’s test mode before going live.
- Switch your Paystack account to live mode once the test order works.
The Checkout Errors Nigerian Stores Hit Most
“Payment provider not available” at checkout
This usually means your store’s country setting does not match a country where Paystack is available. Merchants have reported that the Paystack option disappears when the store location is switched away from Nigeria, so check your store’s location first.
Customers cannot proceed to pay
Your products must be priced in a currency your Paystack account supports. If your Paystack business supports naira but your products are priced in US dollars, customers will not be able to complete payment.
Order stays on “Payment pending”
This is rare, but it can happen if the redirect from Paystack back to Shopify fails, for example after a network timeout. Check the transaction in your Paystack dashboard, and if the payment was received, mark the order as paid in Shopify.
What It Costs
When you use a third-party gateway instead of Shopify Payments, Shopify adds its own transaction fee on top of the gateway’s charges: 2% on the Basic plan, 1% on Grow, 0.6% on Advanced and 0.2% on Plus. On ₦1,000,000 in monthly sales through Paystack on the Basic plan, that is ₦20,000 to Shopify, before Paystack’s own processing fee. Higher plans reduce this surcharge, which matters more as your sales grow.
Frequently Asked Questions
Can I use Shopify Payments in Nigeria?
No. Shopify Payments is not available for stores in Nigeria, so Nigerian stores connect a third-party provider such as Paystack or Flutterwave.
Will customers be able to pay by bank transfer or USSD?
That depends on the payment channels enabled on your Paystack account. Shopify passes the payment to Paystack, and Paystack decides which options to show.
Do I pay Shopify extra when I use Paystack?
Yes. Shopify charges a transaction fee on orders paid through third-party gateways, from 2% on Basic down to 0.2% on Plus, in addition to Paystack’s own fee.
Can I use more than one payment method?
Yes. Shopify lets you offer a primary provider alongside additional gateways and manual methods, and each appears as an option at checkout.
Need your Shopify checkout working properly?
Lifehampers builds Shopify stores with payments set up the right way for Nigeria. See our Shopify developer services or book a consultation.