The adsorption capacity of coal is a crucial criterion for CO2 sequestration in deep unminable coal seams. Previous studies have documented how indigenous microorganisms interact with supercritical carbon dioxide (ScCO2) in coal. But how these interactions affect the adsorption capacity were rarely investigated. In this study, we treated bituminous coal samples with ScCO2-H2O and ScCO2-H2O-microorganism interactions in high-pressure reactors for 120 days at 35 °C and 10 MPa, respectively. After the treatments, we characterized both coal pore types and structures. The comparisons between two different post-treatments indicate that no significant change in coal pore types but notable alterations in pore structures are observed. Specifically, the treated coal with microorganisms exhibits a significant increase in micropore specific surface area (SSA) and surface roughness than the one without them. However, changes in meso/macropore structures and overall pore complexity of the coal sample treated with microorganisms were less pronounced than in coal sample treated with ScCO2-H2O alone. FTIR spectra analysis indicated that the absorption peak intensity of oxygen-containing groups and aliphatic functional groups in the sample treated with microorganisms decreased much more significantly than the sample treated without microorganisms. The CO2 adsorption capacity slightly increased in all treated samples at equilibrium pressures below 2.5 MPa. Above this pressure, the coal sample treated with microorganisms maintained a higher CO2 adsorption capacity, while the sample treated without microorganisms exhibited lower CO2 adsorption capacity compared to untreated coal sample. The increased SSA and the reduced oxygen-containing functional groups of coal after the treatment exerted antagonistic effects on CO2 adsorption. These findings suggest that indigenous microorganisms in coal seams affect CO2 adsorption through antagonistic effects, necessitating site-specific microbial assessments.