VAT repayments may be made to VAT registered businesses if they pay out more in VAT on their purchases than they charge on their sales.
This might happen if, for example, you spent a lot on machinery, seeds, agro-chemicals etc but didn't take much money in the early days of trading. You complete a VAT Return every quarter, setting the VAT you have had to pay against the VAT owed to HM Revenue & Customs (HMRC). If a repayment is due to you it will normally be paid direct into your business bank account a month or so after you have submitted the Return claiming it.
If you are eligible to join the Agricultural flat rate scheme you will not account for VAT, complete VAT returns or be able to reclaim input tax.