Holistic farming systems provide designs for the whole farm that make long term sustainable use of nutrients, water, labour, finances and energy. In using organic residues to produce energy, and safely recycling the digested residues back into the farming system, a biogas digester could be a central component of many holistic systems. This paper discusses the influence of environmental, socioeconomic and cultural constraints on the use of biogas digesters in holistic farming systems in Sub-Saharan Africa. In higher altitude areas where maintenance of optimal temperature can constrain anaerobic digestion, floating drum or fixed dome digesters are a better option than flexible balloon digesters because they are less susceptible to temperature changes. If water is a key constraint, rainwater harvesting could be used to reduce the additional labour needed to collect water. If energy is the most limiting resource in the farming system, the optimum use of organic residues might be as a fuel for anaerobic digestion, whereas, if water is limiting, energy production by burning or pyrolysis might be a better option. The bioslurry from anaerobic digestion can be used in fish ponds to produce plankton to feed fish, and can be applied to fertile fields and fields of intermediate fertility, while biochar from pyrolysis is better used to improve the soil in infertile fields. If labour is limiting, it is particularly important that the system design minimises any additional labour needed to process the organic residues on a daily basis, considering trade-offs between labour and other resources. (C) 2014 Elsevier Ltd. All rights reserved.