A 100-day scCO2-H2O-coal-microorganism interaction experiment was conducted in this study to explore the biogeochemical changes during the supercritical CO2 (scCO2) storage in deep water-bearing coal seams. Compared to a control experiment without microorganisms, the presence of microorganisms resulted in a slightly increase in pH but a marked reduction in oxidation-reduction potential (ORP). An increase in Fe2+ ions and decrease in SO42− ions in the experimental group were found to be closely related to microbial mediation, potentially leading to an increase in secondary pyrite. Networked biofilms and N-acetyl-L-leucine as a leucine derivative were only appeared in the experimental group, indicating microbial growth and metabolism. Microbial activities increased the dissolved organic carbon (DOC), accelerated the accumulation of aromatic organic compounds, and diminished macromolecular organic compounds. After scCO2 injection, microbial number and diversity exhibited a sharp decline and gradual recovery. The dominant Clostridium sensu stricto 13 (>50%), Desulfohalotomaculum (>20%) and norank Desulfallas-Sporotomaculum (>9%) may play important roles in the biogeochemical processes of Fe and S through cooperative relationships. Microbial communities resisted scCO2-H2O stress through diversified defense strategies such as spore formation, enhanced leucine metabolism level, and extracellular polymeric substances (EPS) secretion. The recovery of the number and activity of methanogens indicated potential for the biomethanation of sequestered CO2.