Recent studies in the field of concrete materials show that the early cracking criteria in micro-size can occur as soon as the cement matrix becomes hardened. In many ways, these cracks can become macro-size and opened cracks resulting in significant issues for the durability and appearance of concrete structures as water leakage and corrosion. The technique of self-healing using bacteria has recently received attention for its potential applications. However, the effectiveness and the repeatability of this method over a long period have not been clarified. The information on both the survival and the number of bacteria after healing is limited. This paper aims to improve the self-healing ability and repeatability of concrete when using Bacillus subtilis natto. The experimental studies evaluate the effect of biomineralization with lightweight aggregate as the protecting-carrying vehicle, which can control the release of healing fluid through four cracking-healing cycles. The urease activity and the biomineralization of the bacteria with urea as the main carbon source were assessed and the effect of cracking age on the self-healing capacity, associated with the compressive strength improvement was studied. The results obtained from the optical microscope and SEM/EDS analysis indicated the existence of bacteria CaCO3 forming in concrete after four healing cycles. During long duration, bacterial concentration in concrete was determined by microscopic counting method. Based on experimental results, the restoration of the compressive strength confirmed the high self-healing ability of concrete when using bacteria in lightweight aggregate.