The use of biogas for electrical generation can be an attractive solution especially when integrated with high efficiency energy conversion devices such as fuel cells. H2S content in biogas as high as thousands of ppmv and, when using a single shift reformer, CO content of 2-3 %, are the main challenges in fuel cell application. Biological filters seem to offer a cost effective option for H2S biogas clean-up compared with chemical and physical processes. High Temperature PEM (HT-PEM) fuel cell, based on polybenzimidazole (PBI) polymer and phosphoric acid, is a promising technology when using high CO content reformates. Nevertheless, experimental data on such systems are scarce in literature. In this work, a prototypal HT-PEM system fed with biogas using a biofilter and a single shift reformer is described and field tests, aimed to assess the effect of operating conditions on system performance, presented. The results show that syngas CO concentration can be maintained in the range of 0.1 – 1.5 vol.% if the proper set of reformer operating parameters is maintained, while CO effect on fuel cell performance can be minimized, if the cell temperature is increased.