Solid oxide fuel cell systems operating with biogas can be considered an efficient solution for carbon-free energy conversion. Given the efficiency levels at small-scale, a 100 kW range cogenerative system for micro-grid applications was considered in this study. The challenge in employing biomass-derived fuel in solid oxide fuel cells is related to the performance fluctuations due to biomass intrinsic variability. Thus, the exact composition of the fuel may vary in unpredicted ways during the fuel cell lifetime. An uncertainty analysis combined with a design optimization study was conducted on the fuel cell system and it was demonstrated that the deviation in rate of return is statistically significant, and thus robust optimization is needed for designing a system fueled with highly variable biogas composition.