The effect of internal resistance on the electrochemical processes of microbial fuel cell is demonstrated by Electrochemical Impedance Spectroscopy. The decrease in solution resistance and increase in charge transfer resistance influenced the performance of microbial fuel cell over time. To understand the effect of the parameters on the electrochemical processes a lumped equivalent circuit model for activated charcoal based microbial fuel cell and the Equivalent circuit fitting model of Nyquist plot for graphite based microbial fuel cell is adopted. The Equivalent circuit models predicted negligible activation polarization for activated charcoal electrode assembly and significant activation polarization for graphite electrode assembly. The rationale behind this observation could be due to the higher affinity for biofilm formation on activated charcoal in comparison to graphite. The efficiency of the microbial fuel cell went down with time as the electrochemical kinetics predominates over biochemical kinetics. The Maximum power density and current density measured are (i) 8mW/m2 and 103mA/m2 respectively for activated charcoal based microbial fuel cell, (ii) 1015mW/m2 and 11803.5mA/m2 respectively for graphite electrodes based microbial fuel cells. The power density is 7.6 times higher than the literature data of 133mW/m2 for graphite based microbial fuel cells.