You’ve built a beautiful online store. Your products are listed, your shipping is sorted, and you’re ready to take orders. But if your checkout doesn’t offer the right payment options, you’re going to lose people right at the finish line.
Here’s a plain-English rundown of the most common payment options for NZ online stores, what they cost, and what to think about before you choose.
Shopify Payments
If you’re on Shopify, you’ve probably already been prompted to set up Shopify Payments. It’s worth knowing that Shopify Payments is essentially Stripe under the hood, just integrated directly into your Shopify dashboard. That means no separate Stripe account to manage, payouts sit inside Shopify, and you get a slightly cleaner checkout experience for your customers.
The other big reason to use it is that Shopify charges an additional transaction fee on top of your payment processor fees if you use a third-party gateway instead of Shopify Payments. So if you’re on Shopify and haven’t set it up yet, that’s the first thing to sort. It’s available to NZ merchants across all plans, with processing rates that vary depending on which plan you’re on.
WooCommerce Payments
If your store is built on WooCommerce, you’ve got two main options: WooCommerce Payments (now called WooPayments) or the Stripe plugin. Both are built on Stripe under the hood, so the processing technology is the same. The difference is in how they’re set up and managed.
WooCommerce Payments is the native option. It’s built directly into WooCommerce, so setup is simpler and everything sits inside your WordPress dashboard. No separate Stripe account to log into, no API keys to copy and paste. If you want a clean, all-in-one setup without much fuss, it’s a reasonable choice.
The catch is that WooCommerce Payments creates a Stripe Express account rather than a full Stripe account, and it doesn’t give you access to your API keys. That matters if you want to connect to third-party tools like Xero via a Stripe integration, because that connection won’t work without them. You can still connect WooCommerce to Xero directly through a WooCommerce-Xero plugin, but it’s a different route and worth knowing about before you commit.
The Stripe plugin connects to a full Stripe account, which gives you more flexibility. You can access your Stripe dashboard directly, use it across multiple websites, integrate with Xero and other tools, and take advantage of Stripe’s full feature set. For most of the WooCommerce stores we build, the Stripe plugin is what we use and what we’d recommend for most businesses.
The fees are similar across both, though Stripe edges ahead slightly on international transaction rates.
Stripe
Stripe is the gold standard for online payments in New Zealand, and there’s a reason it’s the technology powering both Shopify Payments and WooCommerce Payments behind the scenes. When the two biggest ecommerce platforms in the world build their native payment solutions on top of it, that tells you something. It accepts all major debit and credit cards directly on your website, is trusted by customers, and integrates with pretty much every ecommerce platform going.
You set it up once and it runs in the background. Payments land in your bank account on a rolling schedule, so you’re not chasing anyone. For NZ domestic card transactions, Stripe currently charges 2.65% + $0.30 per transaction, which actually dropped from 3.5% in late 2025, so good news there. International card fees are higher, so check the Stripe NZ pricing page for the latest.
If you only set up one payment method, make it Stripe.
Bank transfer
Bank transfer costs you nothing in processing fees, which makes it appealing, especially for high-value orders where transaction fees add up fast. But it comes with a trade-off: admin time. You’ll need to check your bank feed daily, sometimes more often during busy periods, to confirm payment before you ship or confirm a booking. Miss one and you’ve either shipped without getting paid, or kept a customer waiting.
Bank transfer works well as a secondary option or for B2B clients who prefer it. We wouldn’t rely on it as your only payment method for a busy consumer store.
Afterpay
Buy now, pay later is no longer just a nice-to-have for ecommerce. Customers expect it. Afterpay splits the purchase into four interest-free fortnightly payments for the customer, but here’s the bit that matters for you as the merchant: Afterpay pays you the full order amount upfront. You ship the order, they handle the rest of the repayments.
Afterpay charges merchants a fee per transaction (a percentage plus a small fixed fee), but the exact rate is set in your individual merchant agreement rather than published publicly. It’s higher than Stripe, so factor that into your margins. The upside is that Afterpay customers tend to spend more per order and convert at a higher rate, particularly on mid-to-higher-priced items.
Apple Pay and Google Pay
These are increasingly just how people pay, on mobile and desktop. If someone has Apple Pay or Google Pay set up on their device or browser, they can check out with a tap or a click, no card details to type out. It’s fast, it’s familiar, and it removes friction at exactly the point where people are most likely to abandon.
If you’re already using Stripe, you can enable both within your Stripe settings at no extra cost. They’re processed at the same rate as standard card transactions.
Pull up your analytics and check how much of your traffic is on mobile. It’s usually more than people expect. But either way, this is worth switching on.
So, what should you actually use?
You don’t need to offer everything, but you do need to offer enough. A solid setup for most NZ online stores looks something like this: Shopify Payments or Stripe as your primary processor, After pay for customers who want to spread payments, and Apple Pay and Google Pay enabled for mobile shoppers. Bank transfer can sit alongside these for customers who prefer it.
The goal is to make sure that when someone reaches checkout, there’s a payment option they’re comfortable with, and nothing standing between them and completing their order.
Not sure if your checkout is set up right?
If you’ve got questions about payments on your store, we’re always happy to chat.
gET IN TOUCH HERE