Can I use Shopify Payments in Nigeria?

No. Shopify Payments only runs in about 39 countries and Nigeria isn't one of them, so you can't turn it on. For a naira store you use a third-party provider instead, and that's almost always Paystack through its Shopify app.

Does going headless let me skip Shopify's payment fees?

No. Headless only means you built the storefront yourself; the payment still happens on Shopify's hosted checkout, which your cart links out to. Because that checkout is Shopify's, its third-party surcharge and the Paystack app both still apply.

How much extra does Shopify charge for using Paystack instead of Shopify Payments?

A surcharge that depends on your plan, roughly 2% on Basic down to a fraction of a percent on Plus, and it sits on top of Paystack's own fee. So you're paying two cuts on the same sale. Check Shopify's current pricing before you commit, since the rates move.

Should I use Shopify with Paystack, or a custom store with Paystack?

Shopify with the Paystack app gets you selling fast and hands the shop plumbing to Shopify, at the cost of the surcharge. A custom store like Fasco drops that fee and gives you full control of checkout, but you build and maintain the whole thing yourself. It comes down to how much the fees and the control are worth to you.

How do I add Paystack to my Shopify store?

Install the official Paystack app for Shopify, then connect your Paystack API keys in your payment settings. It takes a few minutes, and from then on Paystack handles the card step inside Shopify's checkout.

Payments on a Headless Shopify Store: Paystack vs Shopify's Own Gateway

I built my merch store as a headless Shopify storefront: my own Next.js frontend sitting on top of Shopify's Storefront API. The question I get most about it isn't the design or the API, it's about the money. If the frontend is mine, can't I plug in my own payment gateway and skip Shopify's cut? I really wanted the answer to be yes. It's no.

Going headless doesn't move checkout off Shopify

Going headless changes who renders the store, not who takes the payment. My frontend builds the cart through the Storefront API, but that cart hands back a Shopify `checkoutUrl`, and I send the customer there to pay. Shopify's checkout is still doing the actual transaction, which means Shopify still decides which gateways I'm allowed to use and still takes its fee. A custom frontend buys you the design and the speed. It doesn't buy you the checkout. I walked through the whole build in Building a Headless Shopify Store with Next.js.

Shopify Payments isn't an option in Nigeria

Most advice online lands on the same tip: use Shopify Payments, the built-in gateway, and you avoid the extra fee Shopify charges for outside providers. Fine advice, unless you're in Nigeria. Shopify Payments runs in about 39 countries and Nigeria isn't one of them, so you can't switch it on. The neat "just use Shopify's own gateway" answer doesn't exist for a naira store. You're on a third-party provider whether you like it or not.

What you actually use: Paystack through the Shopify app

For a Nigerian store, that provider is almost always Paystack. It's an officially supported gateway with its own Shopify app. The old app was pulled back in 2022, so make sure you're on the current one. You install it, connect your keys in the payment settings, and Paystack handles the card step inside Shopify's checkout. Money settles to a Nigerian bank account, usually the next day. If you've read Paystack vs Stripe, this is the same Paystack, just wearing a Shopify plugin instead of living in your own code.

The catch: Shopify's third-party surcharge

Because you're not on Shopify Payments, Shopify adds a cut of its own on top of whatever Paystack charges. It scales with your plan: roughly 2% on Basic, 1% on Grow, 0.6% on Advanced, and a fraction of that on Plus. It sits on top of Paystack's fee, which is around 1.5% locally with a cap. Two fees on the same sale. Small on a cheap order, but real, and it grows with your volume. Rates move, so check Shopify's pricing and Paystack's pricing for the current numbers before you plan around them.

The other route: leave Shopify, run Paystack yourself

The only way to drop Shopify's surcharge is to stop using Shopify's checkout. That means building the store yourself and talking to Paystack directly. That's what Fasco is: a custom Next.js storefront with Paystack wired in, and every payment confirmed by a signed webhook before an order counts as paid. There's no platform fee on top, and you own how checkout looks and behaves. The trade is that you also own the cart, the admin, and every edge case Shopify used to handle for you. Shopify was doing real work for that fee.

What I'd tell you to do

If you want to be selling next week and you're happy to let Shopify run the shop, use Shopify with the Paystack app and treat the surcharge as rent. If fees matter at your volume, or you want checkout to feel like your product instead of Shopify's, build it custom and run Paystack directly. And if you're going headless for the design freedom, do it, just don't do it to escape the fee. The frontend is yours. The checkout, and the cut, are still Shopify's.