Carbon capture and storage (CSS) technology has the potential to inadvertently release large quantities of CO₂ through geologic substrates and into surrounding soils and ecosystems. Such a disturbance has the potential to not only alter the structure and function of plant and animal communities, but also soils, soil microbial communities, and the biogeochemical processes they mediate. At Mammoth Mountain, we assessed the soil microbial community response to CO₂ disturbance (derived from volcanic ‘cold’ CO₂) that resulted in localized tree kill; soil CO₂ concentrations in our study area ranged from 0.6% to 60%. Our objectives were to examine how microbial communities and their activities are restructured by extreme CO₂ disturbance, and assess the response of major microbial taxa to the reintroduction of limited plant communities following an extensive period (15–20 years) with no plants. We found that CO₂-induced tree kill reduced soil carbon (C) availability along our sampling transect. In response, soil microbial biomass decreased by an order of magnitude from healthy forest to impacted areas. Soil microorganisms were most sensitive to changes in soil organic C, which explained almost 60% of the variation for microbial biomass C (MBC) along the CO₂gradient. We employed phospholipid fatty acid analysis and quantitative PCR (qPCR) to determine compositional changes among microbial communities in affected areas and found substantial reductions in microbial biomass linked to the loss of soil fungi. In contrast, archaeal populations responded positively to the CO₂ disturbance, presumably due to reduced competition of bacteria and fungi, and perhaps unique adaptations to energy stress. Enzyme activities important in the cycling of soil C, nitrogen (N), and phosphorus (P) declined with increasing CO₂, though specific activities (per unit MBC) remained stable or increased suggesting functional redundancy among restructured communities. We conclude that both the direct (microaerobiosis) and indirect (loss of plant C inputs) effects of elevated soil CO₂ flux have significant impacts on the composition and overall structural trajectory of soil microbial populations within disturbed areas.