Despite many technical improvements, concrete still faces quality degradation problems caused by cracks. Many approaches have been studied more extensively, meeting the criteria and realizing that management should be better than preventing the cracks in concrete. With the ability to be easily cultured and form CaCO3, the potential to use Bacillus subtilis natto in full-scale application is promising. Although alkali-tolerant bacteria have been widely studied to maintain enough vegetative cells until the crack formation, their survival is minimal, even when the bacteria were transformed into spores before mixing to concrete. Current works still lack a better understanding of the grave of the factors affecting the fundamental reactions involved, particularly bacterial growth and its bio-mineralization in harsh conditions as concrete. This study clarifies the bio-mineralization of Bacillus subtilis natto with the effects of nutrient-low medium to find a suitable way to protect and maintain the self-healing abilities for a long time. The high survival rate of bacteria immobilized in lightweight aggregate contributes essential information for maintaining self-healing ability at later-age of concrete (durability).