The separator plays a key role on the performance of passive air-breathing flat-plate MFCs (FPMFC) as it isolates the anaerobic anode from the air-breathing cathode. The goal of the present work was to study the separator characteristics and its effect on the performance of passive air-breathing FPMFCs. This was performed partially through characterization of structure, properties, and performance correlations of eight separators presented in Part 1. Current work (Part 2) presents a numerical model developed based on the mixed potential theory to investigate the sensitivity of the electrode potentials and the power output to the separator characteristics. According to this numerical model, the decreased peak power results from an increase in the mass transfer coefficients of oxygen and ethanol, but mainly increasing mixed potentials at the anode by oxygen crossover. The model also indicates that the peak power is affected by the proton transport number of the separator, which affects the cathode pH. Anode pH, on the other hand, remains constant due to application of phosphate buffer solution as the electrolyte. Also according to this model, the peak power is not sensitive to the resistivity of the separator because of the overshadowing effect of the oxygen crossover.