There are 2 types of Flat Rate scheme for VAT – for more details on the standard scheme please see the Flat Rate VAT document.
With the Agricultural Flat Rate scheme you cannot charge VAT but you can add the flat rate addition of 4% to all qualifying sales even if the sales are normally zero rated.
If you are using the agricultural flat rate scheme, you do not have to complete any VAT returns or pay anything to HMRC.
Within Farm Business Cloud you do not have to say that you are VAT registered or complete a VAT return. Just add 4% to any qualifying sales – you should categorise separately it to an income category so that you can keep track of the income that you have made during the year.
Any sales invoices issued should make it clear that it is a flat rate VAT charge so that your customers can claim it back.
See https://www.gov.uk/guidance/agricultural-flat-rate-scheme-notice-70046 for full details.