We show that contact engineering plays an important role to extract the maximum performance from energy harvesters like microbial fuel cells (MFCs). We experimented with Schottky and Ohmic methods of fabricating contact areas on silicon in an MFC contact material study. We utilized the industry standard contact material, aluminum, as well as a metal, whose silicide has recently been recognized for its improved performance in smallest scale integration requirements, cobalt. Our study shows that improvements in contact engineering are not only important for device engineering but also for microsystems.