A three-dimensional multi-component transport model in a two-phase oil-water system was developed. The model includes separated terms to account for the dispersion, convection, injection, growth and death of microbes, and accumulation. For the first time, effects of both wettability alteration of reservoir rock from oil wet to water wet and reduction in interfacial tension (IFT) simultaneously on relative permeability and capillary pressure curves were included in a MEOR simulation model. Transport equations were considered for the bacteria, nutrients, and metabolite (bio-surfactant) in the matrix, reduced interfacial tension on phase trapping, surfactant and polymer adsorption, and effect of polymer viscosity on mobility of the aqueous phase. The model was used to simulate effects of physico-chemical parameters, namely flooding time schedules, washing water flowrate, substrate concentration, permeability, polymer and salinity concentration on Original Oil In Place (OOIP) in a hypothetical reservoir.