Before i became an MOT staion i had this sorted by my accountant but a garage up the road didn't and they got clobbered for £6000 the VATman they only went back 2 years and not the 7 they can do.

As it stands if you charge out what you are charged for an MOT no VAT need be added but it has to be shown seperately you can add a pre inspection fee but this is subject to VAT.

If you make a mark up on the MOT then VAT is due on the whole amount, not just the mark up, this is where the other garage went wrong, his accountant didn't know the rules.

With regard to other non VAT registered work you have done as i understand it when you invoice it out as you are VAT registered tehn the whole amount is liable for VAT that is what i do anyway cannot be wrong that way.
Or just not put it through the books and get the 3rd party to invoice direct to customer that is how we deal with paintwork, as our painter is not VAT registered

Kelly