Carbon dioxide (CO2) sequestration in depleted oil and gas reservoirs is a key technology to mitigate anthropogenic CO2 emissions. In this study, we experimentally investigate the impact of biogeomechanical alteration on CO2 storage in a hydrocarbon-depleted carbonate reservoir using core samples from a deep carbonate formation in the Permian Basin United States. We first obtain the mechanical and microstructural properties of the carbonate samples using the scratch test method, and we treat the samples with a bacteria strain at distinct conditions. Then we expose the samples to CO2 in a supercritical state (ScCO2) for 21 days. We obtain the post-treatment properties of the microbially-treated samples and analyze the effect of the modified properties on long-term CO2 storage in the carbonate formation.