Underground biomethanation, which relies on the subsurface microbial activity to convert hydrogen and carbon dioxide into methane, is a promising approach to support carbon capture, utilization, and storage technology. The process involves injecting hydrogen with captured CO2 into depleted oil and gas reservoirs or aquifers colonized by hydrogenotrophic methanogens that can convert these two substrates into methane. Despite the attractiveness of this technology, there are still uncertainties about the efficiency of the conversion process, particularly the impact of microbial parameters. To investigate the efficiency of the hydrogen conversion process, we relied on a bio-reactive transport model that can mimic microbial growth and decay, consumption of substrates, and transport of reactants and products. It was found that the methane concentration peaks near the injection well when the hydrogen fraction is in the range of 75% to 80% of the injected gas composition. In addition, a noticeable hydrogen sulfide concentration can be produced due to sulfide ions in the brine. Using the Kozeny-Carman relation, an attempt was made to correlate microbial growth with reduced porosity and permeability. It was then revealed that substrate consumption by microbes leads to a drastic increase in the microbial population in the subsurface, which can reduce the petrophysical properties of the reservoir, especially in the near wellbore area. The results obtained from a series of parametric analyses showed that the hydrogen concentration in the injected gas, pressure, well spacing, and injection rate are some of the most important parameters contributing to the biomethanation process.