In this work, the use of fuel cells for valorizing agricultural-derived biogas in Switzerland is studied. The Swiss agricultural case is characterized by farms with small numbers of animals (20 cows) and high feed-in tariffs (FIT) for biogas-derived electricity (0.49 CHF/kWhel). Thus, small-scale biogas installations are reviewed and the possibility to couple them with solid oxide fuel cells (SOFCs) and photovoltaic (PV) panels is analyzed. To date, less than 5% of the Swiss agricultural biogas potential is used. It is possible to increase this value significantly up to 86% through the deployment of 2 kWel engines. The small size of the Swiss farm requires biogas installations in the kW-range. Small-scale biogas facilities are not profitable yet: the main challenge is to bring down the lifetime cost of the fuel cells to 11,000 CHF/kWel (considering a lifetime of ten years) and to reduce the investment cost (IC) of small-scale biogas facilities to around 9500 CHF/kWch. In the kW-range, solid oxide fuel cells (SOFCs) have higher electrical conversion efficiencies than internal combustion engines (ICEs). It is shown that SOFCs become competitive over combustion engines if the investment cost of the former decreases below 13,000 CHF/kWel for a lifetime of 11 years. Combining the biogas facility with a PV-battery system, which covers the digester's electricity needs, is found to be beneficial. A considerable reduction in the feed-in tariffs would make small- to medium-scale biogas installations unprofitable, at current cost. In order to reach a break-even under these conditions, the investment cost of the biogas plant needs to drop below 4000 CHF/kWch, whereas the investment cost of the SOFC needs to drop below 3400 CHF/kWel.