Currently, CO2 sequestration requires a permeable rock mass and a cap rock without major geological discontinuities and fracture network. The complex geological structure and countless faults in Japan significantly limit potential sites for CO2 sequestration, although there are extensive aquifers beneath the ground. To overcome this, the use of microbial-aided chemical reactions is studied in this research project with the aim of enhancing CO2 mineralization in the aquifer as well as of sealing fractures in its cap rock. Although bio-grout with particular types of aerobic microbes has been studied over the last decade in the field of civil engineering to improve the strength of weak soil and reduce the risk of failure, the originality of this study lies in (i) elucidating the effect of chemical reactions enhanced by the enzyme originating from the aerobic microbes on the mechanical behaviour of porous rocks to gain an insight into the possibility of sealing fractures in a cap rock, (ii) screening novel anaerobic microbes that can be used for enhancing CO2 mineralization in a deep aquifer, and (iii) developing a novel numerical simulation method that incorporates enzyme-aided chemical reactions into the coupled fluid-mechanical analysis. It is to be noted that in this project aerobic microbes are studied to investigate the possibility of preconditioning a cap rock with local geological structures, such as fracture network and discontinuities, whilst we examine anaerobic microbes for the purpose of developing a more efficient CO2 mineral trapping technology.