If your client has advised you that they are exempt from paying VAT, usually because they are a charity. You can mark their account as VAT exempt, so no VAT will be added to their invoice.
On the client details tab, half way down the left hand side you'll see VAT Exempt > Click to turn the toggle switch green > Click update to save.
Bear in mind before you give them VAT relief, they will need to give you a written declaration or ‘certificate’ confirming that they’re eligible for the relief. This will usually be in the form of a letter of recognition from HM Revenue and Customs (HMRC).
Accounts Package Settings
If your MagManager account is connected to a third party accounts package eg Xero, you will need to select the correct VAT in the Account Settings:
Go to the main settings page > Under Accounts > Select Xero > Choose your Zero Rated Tax option from the dropdown box > Click Save to update.
The options available to you come directly from your Xero account so may differ from the opions displayed above. If you are unsure which one to choose, check with your accountant.