Underground Hydrogen Storage (UHS) has gained increased importance as a key solution for future green energy economy. However, the equilibrium of hydrogen with mineral-affinitive microorganisms present in underground reservoirs can lead to hydrogen consumption and methane production through the hydrogenotrophic methanogenesis process. This phenomenon not only reduces the amount of stored hydrogen but also affects the safety and economy of this strategy. In this study, geochemical and biological reactions related to hydrogen consumption in underground environments were simulated using PHREEQC software. The model was based on operational and kinetic parameter ranges reported in previous studies, along with the evaluation of methanogenic reactions. Then, 27 different scenarios were simulated in the form of a three-factor experimental design (temperature: 40, 55, and 70°C; pressure: 1500, 2000, and 2500 psi; reservoir rock type: quartz, calcite, and dolomite). The results showed that the least hydrogen consumption and methane production occur at higher temperatures (70°C), higher pressures (2500 psi), and in reservoirs formed from quartz rock. This behavior is justified by the chemical inactivity of the quartz surface and the lack of providing a suitable environment for microbial growth. In contrast, carbonate rocks, especially calcite, due to higher solubility and easier release of metal ions (such as Ca²⁺), create a favorable environment for the enzymatic activity of methanogens. The goal of this project was to identify optimal conditions for hydrogen storage with minimum losses.