Quick Overview: What You Need to Know Before Setting Up Payments
Payment setup is one of the most commonly deferred tasks in e-commerce — it feels less exciting than design or marketing, so it tends to get pushed back. In practice, the range of payment options you offer has a direct impact on your cart abandonment rate and, by extension, your revenue. This guide covers five areas: (1) payment method usage rates and their relationship to cart abandonment; (2) how to activate Shopify Payments and integrate third-party processors; (3) how BNPL services like Paidy and NP Atobarai work, and what to watch out for when setting them up; (4) recommended payment combinations by target customer segment; and (5) how to compare fee structures and set priorities. More payment options isn't always better — the right approach is choosing what fits your customer base.
Why Payment Setup Can't Be an Afterthought
Payment Methods, Usage Rates, and Cart Abandonment
According to Japan's Ministry of Internal Affairs and Communications (MIC) Survey on Telecommunications Usage Trends, credit cards are the most common payment method for online purchases at 76.7%, followed by digital wallet / ID-based payments at 38.5%, and convenience store (konbini) payments at 34.7%. Digital wallet payments have grown considerably in recent years, overtaking convenience store payments and cash on delivery. Meanwhile, the Baymard Institute reports that limited payment options are among the leading causes of cart abandonment — meaning a gap in your payment lineup translates directly to lost sales. Payment setup is as important to revenue as design or customer acquisition.
Activating Payments by Platform
How to Enable Shopify Payments
Shopify includes a built-in payment system called Shopify Payments. To activate it, go to Settings > Payments in your Shopify admin and enter your banking details. Once complete, your store can accept credit cards, Apple Pay, and Google Pay. One important note: if you don't finish your account setup within 21 days of your first sale, Shopify automatically refunds payments to buyers — so complete this setup before your store goes live. For payment methods outside Shopify Payments — such as PayPal, Amazon Pay, convenience store payments, or bank transfers — you'll need to integrate an external payment service such as KOMOJU.
Setting Up Credit Card Payments Through a Payment Processor
There are two ways to accept credit cards on your own e-commerce site: a direct contract with individual card brands, or an aggregated merchant arrangement through a payment processor. Direct contracts offer lower fees but are generally only available to businesses with significant transaction volume. Most e-commerce operators use the aggregated model, which lets you apply to multiple card networks through a single set of documents and consolidates payment infrastructure and settlement management under one service.
How BNPL and Convenience Store Payments Work
Paidy and NP Atobarai: How They Work and What Merchant Approval Involves
Paidy is a buy now, pay later (BNPL) service that lets shoppers pay using just an email address and mobile phone number — no credit card or account registration required. For merchants, Paidy settles on a monthly cycle (paid out on the 20th of the following month) regardless of whether the shopper has actually paid, which eliminates bad-debt risk on the merchant side. Fees range from approximately 3.5% to 6.5% of the sale amount depending on the number of installments, with no setup or monthly fees. NP Atobarai works differently: shoppers receive an invoice with their delivery and pay at a convenience store, bank, or post office — no account registration needed. It's used by major platforms including Rakuten, Animate Online, and minne. Both services typically require one to two weeks for merchant application review, so factor that into your launch timeline.
What to Watch Out for with Convenience Store Payments
Convenience store (konbini) payments open your store to shoppers who don't own a credit card — including younger and older demographics — making them a meaningful way to expand your customer base. The trade-off is that payment timing is entirely up to the shopper, which creates a gap between the order date and confirmed payment. Orders unpaid by the deadline are automatically cancelled. Fees start at around ¥143 per transaction; depending on your contract plan, a minimum monthly fee may also apply, so it's worth modeling your expected transaction volume against these costs before committing.
Recommended Payment Combinations by Target Segment
For Younger Shoppers: Lead with Digital Wallets and BNPL
If your primary audience is younger shoppers who may not have credit cards, prioritize digital wallet options like Amazon Pay and PayPay alongside a BNPL service like Paidy. Offering interest-free installment plans through BNPL significantly lowers the purchase barrier for higher-priced items.
For Older Shoppers and Business Customers: Lead with Credit Cards, Bank Transfers, and Konbini
If your customer base skews older or includes business buyers, leading with familiar options — credit cards, bank transfers, and convenience store payments — is the safe bet. For B2B transactions in particular, bank transfers and services like NP Atobarai that function similarly to invoice-based payment provide a sense of reassurance. If you're targeting overseas customers through cross-border e-commerce, credit card payment is the highest-priority option globally and should be treated as non-negotiable.
Comparing Fees and Setting Priorities
Fee ranges by payment type: credit cards typically start around 3% of the transaction amount; convenience store payments start at around ¥143 per transaction; BNPL services range from approximately 3.5% to 6.5% of the sale amount. Each payment method you add brings incremental fee costs, so the practical approach is to anchor on credit cards first — the highest-usage method — then layer in digital wallets, convenience store payments, and BNPL in an order that matches your customer profile. When evaluating payment services, also check three things: compatibility with your e-commerce platform, security standards and support quality, and a realistic long-term cost projection based on your expected transaction volume.
FAQ
I'm just launching my store — which payment method should I set up first?
Start with credit cards, which rank first in payment method usage according to MIC survey data and are available as a standard option on most e-commerce platforms. Once that's in place, add convenience store payments, digital wallets, and BNPL in an order that fits your customer base — this lets you broaden your reach without overcomplicating your setup from day one.
If I offer BNPL, am I exposed to the risk of non-payment from shoppers?
Most BNPL services like Paidy and NP Atobarai handle their own shopper credit assessment and guarantee settlement to merchants regardless of whether the shopper actually pays. This means merchants carry essentially no bad-debt risk directly. That said, guarantee coverage terms and payment cycles vary by service — review the contract details before signing up.
If I add more payment methods, do my total fees just keep going up?
More options mean more reach, but yes, fees accumulate across each payment method you add. Rather than enabling everything at once, a more practical approach is to prioritize the methods that best fit your customers and product type, then expand gradually as you see results.
Summary
Payment setup may seem like an unglamorous task compared to design or marketing, but it has a direct impact on cart abandonment prevention and revenue growth. Start by anchoring on credit card payments — the most widely used method — then build out your payment mix with digital wallets, convenience store payments, and BNPL in an order suited to your customer base and product type. As you add more options, the design and localization decisions that come with them — especially for international customers — grow more complex as well. Leap supports multilingual e-commerce builds that create an intuitive payment experience for both domestic and overseas shoppers. If you're working through payment design for a cross-border or multilingual EC site, Leap's services are worth exploring.
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References
- Yomuyomu Coloreme "Which payment methods lead to the highest customer satisfaction on EC sites?"
- ROBOT PAYMENT "How to add credit card payments to your EC site: benefits and key considerations"
- ebisumart "EC site payment methods and account setup guide"
- Epsilon "How to choose payment methods"
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- SB Payment Service "What is Paidy? Payment methods, fees, and how it works"
- futureshop "How to make the most of Paidy and what it adds to your EC site"
- futureshop "The case for adding BNPL to your EC site: usage rates, order flow, and setup tips"
- Paymaster Guide "What is BNPL? A complete breakdown of how deferred payment works"
- Japan MIC "2023 Survey on Telecommunications Usage Trends (Household Edition)"
- Baymard Institute "Cart Abandonment Rate Statistics"
