The use of fuel cells for valorising agricultural and food-waste-derived biogas in Switzerland is studied. The Swiss agricultural case is characterised by farms with small numbers of animals (20 cows) and high feed-in tariffs for biogas derived electricity. Thus, small-scale biogas installations are reviewed and the possibility to couple them with solid oxide fuel cells and photovoltaic panels is analysed. It is shown that solid oxide fuel cells become competitive over combustion engines if the investment cost of the first decreases to 13,000 CHF/kWel with a lifetime of 10 years. However, a small-scale biogas installation is not profitable yet: the main challenge is to bring down the lifetime cost of the fuel cells and to reduce the investment cost of small-scale biogas facilities to around 6,000 CHF/kWch. The case of equipping the EPFL and UNIL sites with a digester and a solid oxide fuel cell is examined and is considered feasible from a technical and legal point.