The utilisation of renewable energy has surged over the past decades due to shifts in climate patterns and the diminishing reserves of fossil fuels. Among the renewables, hydrogen energy has emerged as a promising clean energy carrier in recent years. In the hydrogen industry, storage faces a notable hurdle due to the relatively low density of hydrogen gas (0.0813 kg/m³ at 25 °C and 1 atm) and its lower storage density (7–27 kg/m³ at 25 °C and 100–400 atm). As a potential remedy, underground hydrogen storage emerges as a viable option, even though it is not without its challenges. Among these challenges, a prominent one involves the diversity in the composition and physical properties of the reservoir due to the influence of both biological and geo-chemical reactions. In this study, an extensive modelling effort was undertaken to gain insights into the impact of both bio and geo-chemical reactions, variations in porosity, hydrogen depletion, and the effects of diffusion across various levels of salinity, pressure, and temperature. Diverse Water/Rock ratios, distinct minerals, and residual gases were also considered. The modelled conditions encompassing mineral properties and parameters led to a cumulative hydrogen loss of 8.38% over a century. From this, 2.31% was identified due to the reactivity in reservoir rock and 6.07% due to the aqueous diffusion to cap rock and its reactivity. Among these reactions, carbonate dissolution emerged as the most noteworthy, resulting in considerable hydrogen loss contingent upon the presence of methanogenesis bacteria. As per the modelled scenario, porosity was reduced in reservoir rock by 0.41%, and in carbonate cap rock, it was increased by 56%, which could increase the hydrogen leakage. Also, methane (CH4) exhibited the most favourable characteristics as a cushion gas due to its lower reactivity. However, it's crucial to acknowledge that these figures could significantly fluctuate based on variations in mineral composition, bacterial populations and their growth, and the prevailing subsurface conditions. These modelled findings can serve as a valuable tool for comprehending the mechanisms of hydrogen loss and mineral reactivity within a given underground system.