In 1998 it was decided to convert part of the Estate for organic farming to protect the local wild-life and ensure the long-term fertility of the soil. The organic farm extends to about 3200 acres, of which 1200 acres is permanent pasture. This is grazed by a herd of British Longhorn cattle, renowned as a breed for its high quality beef, and flocks of Southdown and Norfolk Horn sheep and deer in the deer park. The remainder of the organic land fits within a rotation producing wheat, barley, vegetables, as well as fodder for the animals. An outdoor pig unit and free range poultry unit also occupy areas within the organic farm.

Conservation has always been an important factor at Houghton. The whole Estate is managed to a policy agreed with Natural England. This helps maintain healthy populations or many species which are becoming rarer, such as skylarks, English partridge and barns owls as well as a wide array of flora and fauna.