The deterioration of concrete structures due to microcracking and ingress of aggressive agents remains a major challenge in construction durability. Recent advances in self-healing technologies demonstrate that the integration of microbial agents and nano-additives offers a promising solution to enhance service life. This study investigates a synergistic approach combining bacterial spores of Bacillus subtilis with nano-silica and nano-calcium carbonate as healing agents within concrete. Upon crack formation and moisture ingress, the bacterial activity precipitates calcium carbonate, while nano-additives improve nucleation, refine pore structure, and accelerate the healing process. Experimental evaluation focused on compressive and tensile strength recovery, water permeability reduction, and microscopic crack closure. Results indicate that bacterial–nano hybrid systems achieved up to 80% healing efficiency for cracks under 0.5 mm, with significant improvements in durability indices compared to conventional self-healing approaches. The findings suggest that microbial–nano synergy is an effective and scalable pathway for developing sustainable, long-lasting infrastructure.