Heritage structures embody past civilizations’ cultural, historical, and social identities and face significant preservation challenges due to crack propagation and environmental degradation. Traditional conservation methods, such as lime mortars, often provide limited long-term protection. This study investigates the incorporation of Bacillus halodurans in lime mortar to enhance carbonation and compressive strength as a potential solution for heritage conservation. Varying concentrations of live and dead bacterial cells (105, 107, and 109 cells/mL) were incorporated into the lime mortar, and their effects on compressive strength and carbonation depth were evaluated over 7, 14, 28, and 56 days. Results showed that live bacterial cells, initially on the 7th and 14th day, reduced carbonation depth compared to the reference mortar. However, by day 28, the sample with 109 cells/mL exhibited a significant increase in carbonation depth and compressive strength, attributed to bio-mineralization and crack self-healing. In contrast, mortars with dead bacterial cells demonstrated less pronounced effects, with the 107 concentration showing the highest carbonation depth but remaining lower than the reference mortar. These findings suggest that bacterial incorporation into lime mortar offers a sustainable and effective method for improving the durability and longevity of heritage structures, providing an innovative alternative to traditional restoration techniques.