As the most challenging problem of concrete, cracking does not only reduce the mechanical properties, but also jeopardize the durability and service life of concrete. Currently, to enhance the lifespan of concrete, self-healing systems are embedded in the concrete and make the concrete be capable of healing the microcracks by itself. A self-healing system that employ bacteria to heal the microcracks is a promising approach. In the present study, the authors utilized the lightweight aggregates (LWAs) impregnated with the solution of Bacillus pseudofirmus B-4104 as a bacteria-based self-healing system. After the healing process, the obtained results indicated that the specific self-healing system could achieve 112% mechanical recovery of the splitting tensile strength, decrease 82% of the gas permeability and 87.4% of the water sorptivity. Thorough investigation by scanning electron microscopy (SEM) combined with Energy Dispersive X-Ray Spectroscopy (EDS) uncover that it is the crystalline healing products at nanoscale that fill the microcracks and eventually healing the samples. Moreover, the healing product showed good compatibility with the cement matrix and regular cubic crystallinity. Further investigations are necessary to establish a relationship between the crack width and the healing efficiency of this bacteria-based self-healing system.