Just to try and be helpful here (the QB help and QB team on the forum just say use the HMRC tools but with no explanation of how you do this).
So here's what I believe you have to do (I have just done this so not got full confirmation from HMRC yet)
1. Download the HMRC basic tools and install it (note it is NOT an online tool you need to install it)
2. Set up your company as an employer in the tool. You will need payroll reference number and company details like reg no.
3. Set up one employee (I know you probably already told the revenue they have left before you realised that QB could not close down the payroll didn't you!). But you have to have told the tool that all employees have left the company before it will let you send the payroll closure message. So set the employee up and set a leaving date for them as per your entries in QB.
4. You should now be able to do the close down payroll, it will ask you to do a final submission so do this. You should then get a message to say the payroll is closing down. But you will then need to submit the final submission so that the revenue are notified.
5. The company should now show a status of Ceased in the tool. You should get a notification to your email to tell you of the submission.
Hope this helps
