Biogenic natural gas is estimated to be 10% of the total natural gas resource in the United States. Significant research advances have been made towards engineering ideal nutrients for optimizing microbial populations that enhance methane generation from coal in laboratory environments. To transition the technique from laboratory to field applications, it is essential to study the geomechanical and flow behavior of coal during the bioconversion process. This study presents the experimental and modeling studies used to estimate permeability changes of coal during continued bioconversion. Several important results are established in this study. First, the capacity of coal to generate methane from bioconversion is not affected by its size, powdered sample versus fractured core. Second, the coal cleat compressibility increases with bioconversion, while the absolute permeability decreases. Third, the rate of bioconversion depends directly on the cleat porosity of coal. Finally, we established that the permeability decreases because of irreducible water saturation before and after the bio-treatment, swelling of coal due to produced methane, CO2 and water, and generation of fines. We propose that irreducible water saturation and swelling would not adversely affect coal permeability in situ given that most US coals are water saturated to begin with. The overall results point to a promising prospect of field application of the technology.