Shopify payments setup in Japan – let shoppers pay the way they usually do

Shopify payments basics: Shopify Payments and third-party providers

Payments on Shopify are built from two parts: Shopify Payments and third-party payment providers installed as apps. Knowing the difference makes it much easier to pick the right combination for your store.

• Shopify Payments: Shopify's own payment service. It covers Visa, Mastercard, JCB and American Express, plus Apple Pay, Google Pay and Shop Pay, and you activate it from the admin
• Third-party payment apps: providers such as KOMOJU, Amazon Pay and Paidy, added from the Shopify App Store to offer konbini, PayPay, pay-later and more
• Manual payment methods: bank transfer or cash on delivery, where you confirm payment yourself

If you run a store on third-party providers only, Shopify adds its own transaction fee on top of the provider's fee. The usual setup is therefore Shopify Payments for cards and wallets, with apps filling the gaps. For the bigger picture, see starting a Shopify store in Japan.

Payment methods Japanese shoppers expect

The right mix depends on what you sell and who buys it. These are the methods that matter most in Japan:

• Credit cards: the foundation. JCB is far more common in Japan than in most markets
• Konbini payment: paying in cash at a convenience store, popular with younger buyers and people trying a new shop without sharing card details
• PayPay and other QR payments: widely used for everyday purchases and a strong option for shoppers on smartphones
• Amazon Pay: buyers check out with the address and card already saved in their Amazon account, which lowers friction at a store they do not know yet
• Pay-later (Paidy, NP Atobarai): customers pay after the goods arrive – useful for gifts and higher-priced items
• Bank transfer and cash on delivery: still in demand for B2B orders and older customers

You do not need all of them. Cards plus Apple Pay and Google Pay, then two or three methods chosen for your customers, usually covers most buyers without cluttering checkout. For payments beyond Shopify, read how to choose e-commerce payment methods.

Adding konbini, PayPay and pay-later to Shopify

Methods beyond cards are usually added through payment apps. Each provider runs its own review, which can take from a few days to a few weeks, so apply early and plan back from your launch date.

• KOMOJU: adds Japan-specific methods such as konbini, PayPay and Pay-easy bank payments under one contract
• Amazon Pay: apply through the official Shopify app and connect your Amazon Pay account
• Pay-later: services such as Paidy or NP Atobarai. The provider usually collects payment from the buyer, so you do not carry the risk of unpaid orders
• Stripe: Shopify Payments itself runs on Stripe's infrastructure, so for card payments in Shopify checkout, Shopify Payments is the standard route

If you need Stripe outside Shopify – subscriptions, invoices or booking payments on a separate site – see Stripe payment integration. Always check each provider's current documentation for supported methods and fees.

How to set up Shopify payments and what to prepare

Payment setup lives under Settings → Payments in the Shopify admin. The steps look like this:

• Business details: company or sole proprietor, representative, address and the bank account for payouts
• Activate Shopify Payments: choose which cards and wallets (Apple Pay, Google Pay, Shop Pay) to show
• Add payment apps: install konbini, PayPay, Amazon Pay or pay-later apps and apply for each provider's review
• Update your legal notice: the page required under Japan's Act on Specified Commercial Transactions must list payment methods, payment timing and any fees
• Test orders: use test mode or a small real order to check payment, order emails and refunds end to end

Have ready: ID documents, payout bank details, product pages and the content of your legal notice. Providers usually check that your store shows products, prices, return terms and business details, so it saves time to build the store and apply for payments in parallel.

Common payment pitfalls

Connecting a payment method is only the start. Check these points before launch:

• Unpaid konbini or bank transfer orders keep stock reserved – set a payment deadline and a cancellation rule
• Order emails do not explain clearly how to pay at a konbini, so support questions pile up
• A newly added payment method is missing from the legal notice page
• A provider review is not finished by launch day, so the store opens with cards only
• Refunds and cancellations work differently for each method, so handling them takes longer than expected

Online stores in Japan are also expected to support EMV 3-D Secure for card payments. Shopify Payments supports it; if you use other providers, confirm their support as well.

How UNANOBO sets up Shopify payments: a free demo first

Before you commit, UNANOBO builds a free demo of your Shopify store based on your brand and products. You see the path from cart to checkout and how payment methods are presented, and decide whether to go ahead once you like it.

For payments, we propose the combination of Shopify Payments and third-party providers that fits your customers and products, then handle the preparation for each provider's review, the legal notice, order email wording and test orders. Payment contracts and payout accounts stay in your name. The founder handles every project personally, from the first demo to improvements after launch, and everything runs by message in Japanese or English.