VAT Only invoices may be required if your registration is delayed and you need to charge a customer VAT in relation to an invoice that has already been sent to them excluding VAT. At present, there is no way of entering a 'VAT Only' invoice in the system. The recommended approach is as follows:
1. Enter the original Sales Invoice net of VAT. If the VAT Rate field is visible in your line item, assign the No VAT code.
2. When you become VAT registered, create a VAT Status in the Settings of your organisation.
3. Create a Credit Note for the same amount as the original invoice using the No VAT code in the line item.
4. Create a new Sales Invoice for the original amount but use an appropriate VAT Rate such as 20% Income in the line item. The total of the new invoice should be the original invoice plus the VAT amount.
5. Allocate the Credit Note from step 3. to the Invoice from step 1.
This method has been confirmed with HMRC and will result in the correct VAT and accounting treatment.