In recent years, biological mineralization has been implemented as a viable option for the elaboration of new building materials, protection and repair of concrete by self-healing, soil stabilization, carbon dioxide capture, and drug delivery. Biogenic mineralization of calcium carbonate (CaCO3) induced by bacterial metabolism has been proposed as an effective method. The objective of the present study was to characterize the bioprecipitation of CaCO3 crystals by Bacillus subtilis in a semi-solid system. The results show that CaCO3 crystals were produced by day 3 of incubation. The prevalent crystalline polymorph was calcite, and in a minor proportion, vaterite. The presence of amorphous material was also detected (amorphous CaCO3 (ACC)). Finally, the crystallinity index was 81.1%. This biogenic calcium carbonate does not decrease pH and does not yield chloride formation. Contrary, it increases pH values up to 10, which constitutes and advantage for implementations at reinforced concrete. Novel applications for biogenic calcium carbonate derived from Bacillus subtilis addressing self-healing, biocementation processes, and biorestoration of monuments are presented.