Although the original question was about income tax (IT) the thread now seems to be chiefly concerned with VAT. The starting point for both is the same. In order to be registered for VAT or IT the beekeeping needs to be run on a commercial basis. There are technical tests for this but common sense is as good a measure as any. Would an independent individual looking at the business and its trading results consider the beekeeping to carried out with the intention of making a profit. It is not necessary to have made a profit but the intention to do so should certainly be there.
Assuming that there is commercial intent we need to consider VAT registration. As has previously been said, VAT registration is compulsory when the turnover of the business exceeds the VAT registration threshold in any 12 month period. The threshold changes each year, mostly on 1st May, and is currently set at £79,000. For beekeeping the turnover would represent all sales of bees, honey, hives/nucs and other bee by-products. The measure is always 12 months long, it does not matter if turnover in any single quarter is significantly higher than £19,750 (£79k /4). The measure is always made to the last day in a calendar month adding up the sales over the previous 12 months. This is repeated on the last day of every month
For beekeeping there are no sales which would be exempt from VAT. All sales would be standard or zero-rated. The difference between zero-rated and exempt is therefore not relevant here. (but for information only when exempt sales are made the amount of VAT which may be recovered on purchases is restricted)
A trader may choose to register for VAT voluntarily before reaching the £79.000 threshold. Provided the beekeeper can demonstrate that they are trading commercially HMRC must accept their registration.
Once registered for VAT the trader must charge their customers VAT and then account for VAT to HMRC on their standard rated sales. The trader may deduct from the VAT on their sales any VAT incurred on their purchases during the VAT period (typically a quarter but could be monthly or annually by election). Where the sales are chiefly zero-rated as would be the case for sales of honey, bees or non-EU sales this would often result in a repayment claim.
When repayment claims are made on a frequent basis it is usual, and in my opinion right, that the trader is selected for checking by HMRC. This could be conducted by phone or more usually a visit from an HMRC Officer. An honest trader should have nothing to fear from such a visit, the Officers in my experience are friendly, knowledgeable and helpful. They are not there to 'catch out' a trader or solely to maximise the Revenue's purse but are there to make sure that all is being done correctly.
Given that a commercial beekeeper after the initial capital purchases does not have a large outlay in consumables there is probably not a lot of purchase VAT which is available to recover until the size of the business is large. I would suggest that it would probably not be worth the effort of being registered for VAT until sales exceed say £25,000. However each business should be considered on its own merits
VAT is fundamentally a straight-forward tax but can seem confusing to those coming to it afresh. Indeed beekeeping is a more complicated trade from a VAT perspective than most. However excellent advice can always be obtained by calling the HMRC VAT advice line 0300 200 3700
I hope that the above is of use, anyone would be welcome to PM me if they need any clarification or further advice
Jack
My background - In addition to being a hobby bee-keeper I am a qualified accountant and tax adviser have run my own accounting practice for more than 20 years.