Sometimes an application for VAT registration can be delayed, and you end up completing work after the VAT start date you asked for, but before the VAT number is known.
You cannot charge VAT to a customer until you have your certificate of VAT registration and you know the VAT number.
If you can delay your first invoices then that’s easier, but you may want to invoice in order to collect the fees first, and to collect the VAT later. You should keep you customer informed of this dilemma.
In situations like these, it becomes necessary to issue a later “VAT only” invoice as soon as the VAT number is known.
There are several examples of invoices on this Excel file and the final one shows you how to set out a “VAT only” invoice.
When sending it to the customer it’s best to remind them that you are simply following the HMRC rules. You have a legal duty to do it this way and they have a legal duty to pay you the VAT!