The use of heat- and alkali-resistant bacteria is essential for the biological repair of damaged concrete. Lysinibacillus boronitolerans YS11 was isolated from the rhizosphere of Miscanthus sacchariflorus. The increased pH in the urea-minus condition during the growth of the YS11 strain promoted calcium carbonate (CaCO) formation. To identify the optimum medium that promoted the growth of the YS11 strain, a Plackett-Burman design was conducted for the screening process. Consequently, malt powder, rice bran, (NH)SO, and corn syrup were chosen to enhance YS11 growth. The optimization of these four useful factors was carried out using a central composite design. To obtain higher survivability in mortar, the sporulation process is essential, and additional factors such as Mn, Fe, and Ca were found to contribute to sporulation. A mixture of L. boronitolerans YS11 spore powder, cement, paste, sand, yeast extract, calcium lactate, and water showed a healing effect on a 0.3 mm mortar crack in 7 days. Furthermore, calcium carbonate precipitation was observed over the crack surface. Thus, we confirmed that mortar treated with YS11 spore powder was effective in healing micro-cracks in concrete.