Basalts are recognized as one of the major habitats on Earth, harboring diverse and active microbial populations. Inconsistently, this living component is rarely considered in any engineered operation carried out in these environments. This includes carbon capture and storage (CCS) technologies that seek to offset anthropogenic CO2 emissions into the atmosphere by burying this greenhouse gas in the subsurface. In this study, thanks to the Carbfix consortium (https://www.or.is/english/carbfix-project), we have carried out the first microbiological survey of a basaltic CCS site associated with the geothermal powerplant of Hellishei (SW Iceland). We show that deep ecosystems were first quickly responsive to field operations associated with pure CO2 injections. Acidifying CO2-charged groundwaters resulted in a marked decrease in microbial richness while lithoautotrophic iron-oxidizing betaproteobacteria together with degraders of aromatic compounds bloomed, hence impacting the redox state of the aquifer and the carbon fate. We show in particular that host-basalt dissolution was key in releasing nutrients and energy sources sustaining autotrophic and heterotrophic growths with possible consequences of the stimulated microbial activities on mineral storage. Then, injections of CO2/H2S/H2-charged groundwater led to clogging at depth. A curative airlift pumping allowed to remove material that was responsible for the loss of transmissivity in the injection well. The associated microbial diversity revealed a strong increase of biomass and a loss of diversity compared to pre-clogging communities. Sulfur-oxidizing autotrophic Thiobacillus sp. and sulfur-reducing Desulfurivibrio sp. were the main representatives of the clogging population. Microscopic observations and spectroscopic analysis highlighted that the injected H2S has reacted with Fe-bearing minerals to abiotically form Fe-sulfides that supported bacterial growth, resulting in dense biofilms aggregating individual oxidized nanopyrites. Oxidation byproducts were also found in the form of large crusts of cell-entombing Fe-(oxi)hydroxides. The stimulation by sour gas injection of specific microbial activities converted submicrometric Fe-sulfides into compact submillimetric microbially-induced mineralizations filling with biofilm the basalt porosity with a likely deleterious impact on well injectivity.