Hydrogen, converted from renewable energy sources, provides a feasible road map to balance the daily up to seasonally fluctuation between renewable energy supply and consumer demand. Underground hydrogen storage (UHS) in porous formations is promising since depleted hydrocarbon reservoirs and aquifers are widespread worldwide, and have a large capacity to meet the G-TWh storage demand. However, unlike underground natural gas (mainly methane) storage, hydrogen is highly susceptible to microbial metabolisms, which can consume and convert hydrogen into other molecules such as methane through methanogenesis. This poses a risk of hydrogen loss and contamination. Another concept is geo-bio-methanation directly in the subsurface, enabling stable long-term storage. Both concepts require a thorough understanding of microbial activities within porous rocks. The key questions, including, 1) does microbial growth reduce reservoir performance? 2) is there any effect of minerals and pore microstructures on microbial activities? 3) how do static and flow conditions affect microbe distribution? need to be better elucidated. To tackle these questions, we develop an unconventional real-rock micromodel configured with a thin rock layer in a transparent microfluidic chip. This innovative setup allows us to visualise microbial growth in rocks under a fluorescence microscope. By employing real-rock micromodels, we can overcome limitations related to mineral homogeneity and artificial pore structures. Consequently, this workflow and platform may hence offer new possibilities for studying microbial metabolism in geo-materials and the potential interactions.