Renewable sources of energy can help mitigate global warming. One of the most significant drawbacks of renewable energy is the disparity between supply and demand. Geological hydrogen storage is a way to overcome this imbalance as it provides a way to store hydrogen as a source of energy and reproduce it during periods of energy shortage. Hydrogen can be then be stored either in depleted gas reservoirs or in deep saline aquifers. A high concentration of hydrogen in the subsurface can trigger its consumption by in-situ microorganisms. That is why it is essential for us to understand the microbial metabolism of hydrogen. Although microbial consumption of hydrogen is known from the literature, a quantitative assessment that shows the extent to which the consumption takes place is somewhat lacking. In this study, we investigated in the first place the main influencing parameters of in-situ hydrogen conversion, namely hydrogen conversion into methane (CH4) when it is co-injected with carbon dioxide or when CO2 is already present in the medium, a process known as methanation. It is known that methanation and sulfate reduction (a process in which hydrogen is transformed into hydrogen sulfide (H2S) in the presence of sulfate) are some of the major microbial metabolisms happening during hydrogen subsurface storage. In the next step, we studied the plume migration of injected gas to investigate the presence of sweet spots for hydrogen, carbon dioxide, and methane. This was followed by an interpretation that estimated the time step at which a steady-state flow for each gas is achieved. After that, we considered different reservoir conditions under which hydrogen can be stored, and we estimated the recovery rates of hydrogen, methane and hydrogen sulfide. In our last step, we investigated the influence of microbial population growth on rock porosity and permeability by numerical simulations.