Nowadays there is an interest in the energy sector in the underground bio-methanation technology. It has such great attention due to high subsurface volumes and variable conditions for the bio-methanation process which makes this technology promising. However, the feasibility of the technology needs to be studied with more precision. Which also include the estimation of the methane yield out of field scale project. The addressed questions in the thesis are related to optimal design criteria for the methanation, uncertainty in the microbial kinetic parameters, hydrogen and carbon dioxide conversion and the methane yield. A two-phase multicomponent bio-reactive transport model for simulation of the bio-methanation is implemented. The C++ code was used from the open-source multi-physics simulator DUMUX and improved for a field-scale needs. Several designing criteria for the process were proposed both for new operations, re-using of depleted gas fields, and underground storages with nitrogen as cushion gas. It was shown that there is a huge gap in understanding microbial kinetic parameters. At the same time, it has a major effect on the kinetics of the microbial distribution and hydrogen conversion. Finally, the results from a field-scale model simulation are presented. And the total methane yield is estimated.