To mitigate climate change and adopt renewable energy, energy storage is crucial and can be done in the form of hydrogen gas (H2). Subsurface geologic reservoirs are positioned to store H2 on the largest scales for the longest terms of all potential options. However, H2 injection may boost reactions that consume hydrogen, generate undesired gases, and alter pore structures of geomedia. To explore the extent of H2-associated biotic reactions at a near wellbore location, four experiments were conducted under underground storage conditions with wellbore cement cores and, in most instances, shale samples submerged in synthetic formation brine. Post-reaction gas, aqueous, and solid phase samples were analyzed using olfactory screening and, later, gas chromatography (GC-MS), inductively coupled plasma optical emission spectroscopy (ICP-OES), scanning electron microscopy (SEM), and synchrotron micro-scale x-ray fluorescence (μ-XRF). Within a period of 16 weeks, hydrogen sulfide (H2S) was generated in systems containing both H2 and shale. XRF mapping identified a zone enriched in iron(II) and reduced sulfur along the rim of cement cross sections that was largely associated with CO2-induced cement carbonation. Shale did not show noticeable alteration, but there is evidence it contributed to the initial inoculation of the system and provided nutrients for microbes via water-rock interactions. This study considers both rock formations and wellbore cement not previously evaluated concurrently. Findings support understanding and modeling of H2-associated biogeochemical reactions during underground hydrogen storage.