If under IR35 and VAT registered and with the income received already charged Tax and NI how is this recorded in Quick books as I need to issue a VAT invoice ?

Welcome to the Community forum, @fairwayconsultan. 

Let me explain the difference between the IR35, National Insurance (NI), and Value Added Tax in QuickBooks Online (QBO), so we'll learn how to record them correctly.

The IR35 is also known as off-payroll working. There are sets of regulations that govern how contractors are paid. Moreover, this is only available in the QBO Advance Payroll subscription. For more info, you can read the HMRC IR35 guidance.

First off, set up the IR35 in your account. Here's how:

1. From the Payroll, select the Payroll Settings tab.
2. Below the Business settings, choose HMRC Settings.
3. Look for the IR35 contractors.
4. Tap Yes. Then, Save.

Check out this article, for more details: IR35 in QuickBooks Online Advanced Payroll.

Also, NI is under the payroll contribution and only available in QBO Advanced. You must deduct the NI from the employee's wages. If you apply the NI back calculation it will result in the employee being responsible for the underpayment of the NI contribution. 

If you want to create an NI adjustment, you must process an HMRC adjustment via pay run. You can read this article for more info: How to back-calculate National Insurance contributions in QuickBooks Online Advanced Payroll.

To add this to your employee contributions, read the detailed steps in this article: Add, and update an employee record in QuickBooks Online.

On the other hand, VAT is a tax added to the service or product you offer. If you want to add this to your invoice, you'll need to set this up. Here's how:

1. Select VAT from the Taxes.
2. To start calculating VAT, pick a month. Then, choose filing frequency.
3. Pick your accounting method.
4. Type in the VAT registration number. If applicable, select the Flat Rate Scheme (FRS) box and enter the percentage and tax registration date.
5. Click Next, then OK.

Additional details are available in this article: Set up and edit VAT settings, codes, and rates in QuickBooks Online.

You might want to view certain transactions in your account in a report. Check out this article: Run reports in QuickBooks Online.

Leave a comment below if you have additional questions about managing taxes in your account. I'll be willing to help. Keep safe always.