Occasionally you may need to create a "VAT only" invoice.
Please note however that HMRC don't recommend doing this when you're in the process of registering for VAT. They recommend issuing proforma invoices with the amounts shown inclusive of VAT and then re-issuing those invoices when your registration comes through. FreeAgent will do this for you if you choose the setting "Registration Applied For" under Settings > VAT Registration.
If you can't avoid creating a VAT only invoice, create a new invoice and add an invoice item using the new item type VAT and the total amount of VAT in the 'Total Amount' field:
Now, when you view the invoice, you'll see the full amount of this item charged only as VAT:
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