Disclosed are devices, systems and methods for implantable biofuel cells. In some aspects, a biofuel cell device for extracting energy from a biological fluid includes a substrate including two compartments each with one or more openings; an anode assembly disposed in the substrate and including an anode electrode and functionalization material to facilitate an oxidative process that releases electrons captured at the anode electrode; and a cathode assembly disposed in the substrate separated from the anode assembly and including a catalytic material facilitate a chemical reduction process such that the biofuel cell device extracts electrical energy from the substance in the biological fluid.