Carbon capture and storage (CCS) in deep geological aquifers has shown to be the most viable option for mitigating the greenhouse gas effect of carbon dioxide (CO2) at a large scale. However, the underground formations often possess discontinuities in the caprocks, leaking the stored CO2. Potential leakage paths, such as abandoned wells, have been growing due to excessively unplugged oil and gas exploration wells. The leakage of CO2 from these wells is a major concern, considering their negative impact on the environment and compromising CO2 storage efficiency. Recently, microbially induced calcite precipitation (MICP) technology has proven to be an effective and sustainable method for reducing the permeability of geomaterials. Nevertheless, the MICP process involves intricate interactions among bio-chemo-hydraulics (BCH) domains to comprehend the reactive transport of biochemicals. The complex nature of the MICP process poses difficulties in setting the biochemical injection durations for a particular target distance at the given injection rate. Given this, the present study developed a coupled numerical model and employed it as a workable tool for optimising MICP injections to plug the abandoned well connecting two deep geological aquifers. Following that, the study evaluated the leakage of CO2 using flow migration rates in the untreated and MICP-treated leaky aquifer. The study proposed a novel optimisation strategy for biochemical injections under near and far-field leakage conditions. The sensitivity of biochemical injection durations on the attached bacterial amount and permeability in the leak was also determined. The observations from the present study indicated a complete reduction in the CO2 migration rates from the abandoned well due to a reduced permeability after MICP, thereby indicating the efficacy of the proposed optimisation methodology. Further, a cost analysis of the MICP treatment indicated a rational application cost with the target distance compared to the detrimental effects of CO2 leakage.