Microbial enhanced oil recovery (MEOR) is a potential low cost method for increasing crude oil recovery. Before MEOR field applications can be performed with confidence, it is important to understand key mechanisms and quantitative relationships between microbial metabolism, permeability, interfacial tension and residual oil saturation. In this study, a fully coupled finite element model of the MEOR processes in homogeneous and heterogeneous porous media is presented. This model includes biological and hydrological processes and also describes how the interfacial tension reduces the residual oil saturation. Numerical simulations of core flooding experiments are performed to investigate the influence of different bacterial concentrations and types on the oil recovery. Results show that the microbial processes in homogeneous porous media can increase the oil recovery significantly if water containing suitable bacterial concentration and type is injected. Simulations using a sandstone porosity distribution measured via X-ray CT show that the heterogeneity of the rock has a significant effect on the MEOR processes.