Approximately half of the nation's sheep (organic and non-organic) are found on hilly upland areas. Most sheep are able to free range for most of their lives, although some may be brought inside to give birth. Stocking rates will generally be lower on organic farms than other farms.

The big difference between organic and non-organic sheep systems are the methods used to prevent and control diseases. Non-organic sheep are likely to receive many more veterinary treatments than organic sheep. For example many non-organic lambs will be wormed every four to six weeks, regardless of whether they actually have worms.

Organic farmers manage their flocks carefully to reduce the disease risk to new-born lambs and use clean grazing systems to minimise the need for worming. Clean grazing involves managing pastures so that sheep, and particularly lambs, are only put into fields that have very low or no worm infestation. If worming is necessary certain treatments can be used, provided the farmer gets approval from a vet and permission from Soil Association before using the treatment. If a wormer must be used, then those which do not leave residues in the animals' dung are used whenever possible.

Many non-organic farmers also use organophosphorus dips to control sheep scab, which are banned under the Soil Association's rules . Double-fencing can help to prevent sheep scab, which spreads when infected sheep rub on fences dividing them from healthy ones. However, this method is impractical on upland areas. Maintaining a closed flock (no bought-in stock) can also prevent disease.

Ideally organic sheep graze in a rotation with cattle. By moving sheep onto land which hasn't had sheep grazing it the year before means that different grasses are available for the sheep and cattle to eat. This varied diet is good for their health.