Anaerobic digestion processes and the conductive electron transfer approach were used to describe the bioenergy production processes in a microbial fuel cell (MFC), respectively. The present model is a far more completed form of conduction-based modeling which is able to predict performance of an MFC fed with complex substrates and inoculated with multi-population culture. One-dimensional spatial distributions of the different microorganisms, as biocatalysts of processes and intermediates produced in the different steps of the anaerobic digestion processes in the biofilm, as well as the dynamic behavior of the anolyte including syntropic interactions among different groups of microorganisms to degrade organic materials and wastewater were simulated. In addition, a fast convergence and reliable numerical solution was proposed to increase the model's applicability for a variety of simple to complex substrates. Model validation was performed using experimental results from the MFCs fed with glucose, gluconic acid, xylose, arabinose, cellulose, protein and dairy wastewater. Also, MFC performance was assessed by analyzing the microbial activity in the biofilm as biocatalyst and characterizing the anolyte's features. The results obtained from the simulation were compared to some previous models, as well. The results show a promising pathway for modeling the complex nature of bioenergy production in the MFCs. (C) 2015 Elsevier Ltd. All rights reserved.