Microbiological calcium carbonate precipitation (MCCP) has been investigated for its ability to improve the durability of cement mortar. However, very few strains have been applied to crack remediation and strengthening of cementitious materials. In this study, we report the biodeposition of Bacillus subtilis 168 and its ability to enhance the durability of cement material. B. subtilis 168 was applied to the surface of cement specimens. The results showed a new layer of deposited organic-inorganic composites on the surface of the cement paste. In addition, the water permeability of the cement paste treated with B. subtilis 168 was lower than that of non-treated specimens. Furthermore, artificial cracks in the cement paste were completely remediated by the biodeposition of B. subtilis 168. The compressive strength of cement mortar treated with B. subtilis 168 increased by about 19.5% when compared with samples completed with only B4 medium. Taken together, these findings suggest that the biodeposition of B. subtilis 168 could be used as a sealing and coating agent to improve the strength and water resistance of concrete. This is the first paper to report the application of Bacillus subtilis 168 for its ability to improve the durability of cement mortar through calcium carbonate precipitation.