The porous nature of lightweight aggregate and its inherent tendency to crack are two main factors related to the penetration of aggressive ions into the concrete matrix in unfavorable environments easily, causing the concrete to deteriorate and reduce its service life. Although the degrading effect of aggressive ions threatens the cement matrix and reinforcement, the inclusion of bacteria and nutrients in cementitious systems leads to CaCO3 precipitation to fill the pores of the aggregates. In this study, Bacillus Subtilis were impregnated into pumice aggregate with 3 different nutrient media, Tryptic Soy Broth, Modify Luria-Bertani, Urea-Calcium-Phosphate. As a result, glucose-based components in nutrient medium increase air entrainment and create a hollow structure in mortar mixture. However, the presence of urea and Ca2+ in nutrient medium increases the CaCO3 precipitation efficiency of bacteria and filling the pores of pumice. Besides, encapsulation is necessary to protect bacteria viability and improve crack healing.