What to Watch After You Start Taking Payments: Fees, Reconciliation, Refunds, Invoices and Card Fraud

Once your payment gateway is approved and your website starts taking money, you can breathe a sigh of relief 😮‍💨 But there are still a few everyday things to keep an eye on after that: fees, reconciliation, refunds, invoices, and card fraud and scams.

This article goes through them one by one, with sources for everything. Each provider's official rules take precedence.

Who pays the fees?

Transaction fees are paid by the merchant to the payment gateway and are deducted at payout, so the amount you receive is a little less than the order amount.

So can you charge customers an extra “card processing fee”? ECPay says that under transaction management rules, credit card transactions can't carry an extra card surcharge, and you can't refuse cards based on the amount (ECPay registration info). A government interpretation letter from years ago also stated that contracted merchants' fees can't be passed on to cardholders (Executive Yuan website letter) .

The more common approach is to treat fees as a business cost and build them into your product prices 🧮

Payouts: first to your payment gateway account, then to your bank

When a customer pays, the money doesn't reach your bank that same day. There are two stages in between:

• Payout period: until the money becomes withdrawable in your payment gateway account. For example, ECPay regular sellers get it within 10 days after payment (ECPay fees page); NewebPay credit cards are the capture date +10 days and ATM is the payment date +7 days (NewebPay rate table)
• Withdrawal: from your payment gateway account to your bank. ECPay interbank withdrawals cost US$0.48 each; NewebPay costs US$0.32 each, with the first 5 each month free (same sources as above)

Many providers let you set up automatic withdrawals, so once it's set, you don't have to click every time ⏰

Reconciliation: matching orders, payments and your bank

Reconciliation means checking that the numbers match across "orders on your website," "payment records in your payment gateway dashboard" and "deposits in your bank." It's best to do it on a regular schedule, like once a week:

• Export paid orders for the period from your website's admin panel
• Export transaction details for the same period from your payment gateway dashboard, and see how much was deducted in fees
• Compare against your bank passbook or online banking to confirm the withdrawn amounts arrived
• If something doesn't match, first check whether it's a refund, a cancellation, or still within the payout period

The nice thing about taking payments with ATM virtual bank accounts is that each order has its own account number, and the system matches it to the order automatically. That's much easier than asking customers for the last five digits of their account.

How refunds work

With your own payment gateway, you process refunds yourself in your payment gateway dashboard. A few things to know:

• Credit cards: you can usually refund the card directly from the dashboard, but there's a time limit. With NewebPay, for example, credit card and UnionPay card refunds must be made within 89 days of the transaction (Site Now NewebPay summary)
• Convenience-store payment codes and ATM: customers paid by cash or transfer, so refunds often have to be handled separately. NewebPay's FAQ says that when refunding a transaction paid with a convenience-store payment code, the fee isn't returned, and the refund has to be handled by the merchant (NewebPay FAQ)
• Fees: transaction fees already deducted may not be returned when you refund; it depends on each provider's rules

It's best to put your refund policy on your website ahead of time, like how many days customers have to request a refund, how it works and who pays shipping. Customers can see it, and handling refunds is clearer too.

E-invoices

Registered businesses that need to issue invoices must issue one to the customer after receiving payment. Once an e-invoice is issued, it must be uploaded to the Ministry of Finance platform for record within 48 hours, or within 7 days at the latest if the buyer is a business (Ministry of Finance regulations) .

ECPay, NewebPay and other providers also offer e-invoice services that let your website issue invoices automatically after a successful payment; you need to apply for them separately. Under Ministry of Finance rules, selling goods online with monthly sales of US$2,585 or more (US$1,290 for services) requires tax registration. Whether you need to issue invoices yourself is up to the National Taxation Bureau's guidance.

Card fraud and chargebacks

If someone uses another person's card on your website, the cardholder will dispute it with the card-issuing bank once they notice. This is a "chargeback," also called a dispute. The process is roughly:

• The card-issuing bank notifies you through the payment gateway
• The money may be taken back first
• You provide proof such as shipping records, tracking numbers and conversations with the customer
• The bank decides the outcome

Day to day, you can lower the risk like this:

• Always keep tracking numbers and delivery confirmations when you ship
• If one person places a lot of orders in a short time, or the shipping address and details don't add up, contact them to confirm before shipping
• If your payment gateway offers 3D Secure verification or risk-control features, ask them how to turn them on

Watch out for fake notices and fake customers

Scammers target merchants too. Common tricks include:

• Emails or text messages pretending to be from your payment gateway, asking you to click a link to "re-verify your account"
• Someone claiming to be a customer, saying their payment failed and asking you to use an ATM or give them your account details
• Sending a "payment completed" screenshot and asking you to ship first

The safest approach: to check whether a payment went through, only look at the records when you log in to your own payment gateway dashboard. To log in, type the URL yourself or use a bookmark. Don't click links in messages 🔒

Card numbers never go through your website

With payment pages from gateways like ECPay and NewebPay, customers enter their card number on the payment gateway's side, so it never passes through or gets stored on your website. The international card data security standard PCI DSS also says that when merchants hand card processing to a compliant service provider and never handle card numbers themselves, many requirements don't fall on the merchant, though you still need to make sure the service provider itself is compliant (PCI SSC info) .

Quick recap

• Merchants pay the fees, and you can't charge customers an extra card surcharge
• Money goes into your payment gateway account first, then you withdraw it to your bank after the payout period
• Reconcile on a regular schedule: orders, payment gateway and bank
• Put your refund policy on your website; credit card refunds have a time limit
• If you need to issue invoices, your website can issue them automatically
• Only trust the deposits in your own dashboard, and don't click links from unknown sources

Our Small Shop Website booking deposits and event registration fees connect to your own ECPay account, and all transaction records are in your own ECPay dashboard; E-commerce Website every plan includes payment gateway integration (your choice of ECPay or NewebPay). If you haven't applied for a payment gateway yet, start with How individuals, sole proprietors and companies apply for a payment gateway 📚