Bacteria consume electron donors (fuel) which are oxidized to gain energy. This electrochemical reaction and the reduction of terminal electron acceptors typically occur inside the bacterial cells. Microbial fuel cells with a membrane-electrode assembly were modeled under quasi-steady state and non-steady state conditions. The model assumed the presence of a thin biofilm on the anode surface, a diffusion boundary layer, diffusion and consumption of the electron donor in the biofilm, and cross-over of the electron donor through the membrane. The model was based on fundamental theories of mass transfer, electron transfer, and microbial respiration. The results of the modeling explain trends in the experimental data, provide direction for future experiments, and give insights into more efficient MFC designs and operational strategies. This is an abstract of a paper presented at the 2006 AIChE Annual Meeting (San Francisco, CA 11/12-17/2006).