Skip to content

Automatically matching online invoice payments

One of the many benefits of online invoice payments is that you can combine it with the automatic bank transaction matching features in MYOB Business to streamline your payment reconciliation. This help topic explains how automatic matching of online payments works and what to check if your payments aren't auto matching.

What happens when a customer pays you

When a customer makes an online payment, the fees are deducted from the payment and the balance will be settled into your nominated bank account. The payment and fees will be automatically be recorded in your MYOB business, and the associated invoice will be closed off.

You'll receive an email notification about the payment, and the payee also receives an email confirming that they've paid.

How the payment is recorded in MYOB

When you set up online invoice payments, you'll set a Payment account and Fee account. These are ledger accounts in your MYOB software that take care of the accounting side of your online payments and fees.

When a payment is made, the required transactions are automatically recorded in MYOB using these accounts. Then when the funds are settled into your actual bank account, this flows through to your MYOB business in your bank feeds and it'll be automatically matched.

This is known in MYOB Business as auto-reconciliation because it automates the entire payment process.

What transactions are automatically recorded


MYOB automates the online invoice payment process so you don't need to do anything. But if you're interested in knowing what happens behind the scenes, here's a breakdown.

When a payment is made, two transactions are recorded in your MYOB business:

  • a customer payment transaction which closes the invoice, and

  • either a spend money or receive money transaction, depending on whether or not you've passed on the 2.7% surcharge to the customer, and if there is GST on the invoice.

If you pass on the 2.7% surcharge (and there's GST on the invoice)

A receive money transaction is recorded to account for the GST you've collected on the customer's surcharge, and the 25c transaction fee you've paid.

Here's an example:

Example receive money transaction for an invoice with GST

If you pass on the 2.7% surcharge (and there's no GST on the invoice)

A spend money transaction is recorded to account for the 25c transaction fee you've paid. Here's an example:

Example spend money transaction for an online invoice payment transaction fee

After the funds are deposited into your bank account

When the net settlement value (customer payment minus fees) is deposited into your nominated bank account, a bank deposit transaction is automatically recorded to group the above two payment transactions together – the sum of which results in the net settlement value.

This bank deposit transaction will then be automatically matched to the customer's payment in your bank feed.

What can prevent automatic matching?

If your online invoice payments aren't being automatically matched, you'll notice that they indicate that they still need to be allocated on the Bank transactions page.

While you can manually match them, we recommend using the smarts in MYOB to do all the heavy lifting.

Check the following:

  • make sure the option Automatically match bank transactions to MYOB bills and invoices, is selected (go to Banking > Bank rules)

  • make sure you've chosen ledger accounts to record payments and fees. Open the online invoice payments portal and choose the ledger accounts to record payments and fees and click Save. These ledger accounts are part of changes to the way we bill you for online invoice payments.

  • make sure you've set up a bank feed to connect your bank account (where customer payments are deposited) to the MYOB ledger account you've chosen as the Payment account in your online invoice payment settings. You can check this in the online invoice payments portal.

What amounts make up a customer's payment?

To see a breakdown of your customer's online payments, run the Transaction details report (Reporting menu > Reports > Online invoice payments tab).

The amount you receive will be different to the invoice amount because of the fees and charges.

If you need more details about your online invoice payments, see Online invoice payment reports.