How can I fully receive a payment, netted by a customer for IR35, to close the invoice and match PAYE and NI amounts for the relevant employee

Hello there, michael176.

You can combine the payments and add the fees in the Bank deposit window. To create a receive payment for the invoice entered in QuickBooks, make sure to deposit the amount to the Undeposited Funds account.

Here's how:

1. Go to + New > Receive Payment.
2. From the Customer drop-down, choose the customer's name.
3. Select the Payment date, Payment method, and choose the Undeposited Funds account from the Deposit to drop-down list.
4. Under the Outstanding Transactions section, put a checkmark on the invoice you want to pay.
5. Click Save and close.

Once done, let's record a bank deposit to include any fees by following these steps:

1. Go to + New > Bank Deposit.
2. Select the bank account where you want to deposit the money.
3. In the Select the payments included in this deposit section, put a check mark on the payment you want to deposit.
4. Under Add funds to this deposit, select the customer's name from the Received From column.
5. Select an expense account from the Account column, and enter the fee as a negative amount.
6. Click Save and close.

Finally, match the deposit to the payment posted on the Banking page. I'm adding these articles for reference:

• Record and make Bank Deposits in QuickBooks Online
• Categorize and match online bank transactions in QuickBooks Online

Don’t hesitate to reach out if something else comes up, feel free to leave a comment below. The Community and I are always here to help.