Underground hydrogen storage (UHS) is a promising solution for managing energy supply variability and enabling large-scale, long-term energy storage. By storing surplus hydrogen during periods of low demand and retrieving it when needed, UHS enhances energy diversity and operational flexibility, supporting a more resilient and adaptable energy system. However, injecting hydrogen into geological formations triggers a complex interplay of biological and geochemical interactions that extends far beyond conventional considerations of physical containment and deliverability. This review systematically examines subsurface microbial activity and the mechanisms governing microbial and geochemical processes during UHS, including methanogenesis, sulfate reduction, acetogenesis, iron reduction, and their coupled interactions with reservoir mineralogy. We then present a comprehensive synthesis of experimental investigations, ranging from batch reactors and microfluidic platforms to field-scale trials, complemented by computational studies encompassing batch geochemical simulations (e.g., PHREEQC), reservoir-scale reactive transport modeling (e.g., DuMux, CMG-GEM, Eclipse), and molecular dynamics simulations of interfacial and wetting behavior. Field observations from historical town gas storage sites and ongoing UHS pilot projects worldwide are critically evaluated to bridge the gap between laboratory findings and real-world subsurface behavior. By integrating findings across disciplines, we identify persistent knowledge gaps, particularly regarding the kinetics of long-term microbial and geochemical reactions, spatiotemporal variability, scale-up from laboratory to field conditions, and feedback mechanisms under dynamic operational cycles. We conclude with a critical appraisal of risk mitigation strategies, including microbial control, site selection criteria, and adaptive monitoring frameworks, offering a forward-looking perspective on the design and optimization of future UHS systems across diverse geological settings.