When a customer makes a payment by clicking Pay securely in their invoice:
the fees are deducted from the payment and the balance will be settled in your nominated bank account within 2 business days
the associated invoices will be closed and marked as Paid, and
the payment and fee will be automatically recorded in the categories you chose when you set up online payments.
Choose categories to record payments
When a customer makes an online payment, it's automatically recorded in the Payment category and Fee category you chose when setting up online payments. These categories take care of the accounting side of the payments and fees, so you don’t have to record them manually.
Typically the Payment category is an asset category that represents the business bank account where your customers’ payments are settled. The Fee category is an expense category that’s there to simply keep track of the fees. Unlike the payment category, it doesn’t represent a bank account.
How the payment is recorded in the app
When a payment is made, everything happens automatically so you don't need to do a thing.
The associated invoice is closed and marked as Paid. Also, the required transactions are automatically recorded in the background using the Payment category and Fee category you specified when you set up online payments. These are categories in the app that take care of the accounting side of your online payments and fees.
You'll see these transactions on the Transactions list report (More > Reports > Transactions list).
When the funds are settled into your actual bank account, this flows through to the app via your connected bank account. These deposits will be automatically matched to the transactions mentioned above, based on the Payment category and Fee category you've specified.
If a customer disputes a payment
If a customer sees a transaction on their bank statement that they don’t think looks right, they can raise a dispute with their bank. If they dispute a payment from one of your sales, we’ll send you an email with details of the dispute.
You’ll need to reply to the email with proof that you supplied the goods or services as was expected and agreed to. The customer’s bank will then review the documentation to determine if the transaction needs to be reversed, also known as a chargeback.