Geological storage of CO₂ is a fast-developing technology that can mitigate rising carbon emissions. However, there are environmental concerns with the long-term storage and implications of a leak from a carbon capture storage (CCS) site. Traditional monitoring lacks clear protocols and relies heavily on physical methods. Here, we discuss the potential of biotechnology, focusing on microbes with a natural ability to utilize and assimilate CO₂ through different metabolic pathways. We propose the use of natural microbial communities for CCS monitoring and CO₂ utilization, and, with examples, demonstrate how synthetic biology may maximize CO₂ uptake within and above storage sites. An integrated physical and biological approach, combined with metagenomics data and biotechnological advances, will enhance CO₂ sequestration and prevent large-scale leakages.