Biomineralization is a universal process that has implications in a variety of areas, from civil engineering to medicine. While crystallization of amorphous CaCO3 formed in vitro is known to precede the vaterite-calcite/aragonite pathway, this process could be significantly altered when induced by bacteria, particularly within the extracellular matrix (ECM) of microbial cells. We used a combination of SEM, SANS, SAXS, FTIR and XRD methods to investigate the structure of CaCO3 formed during biomineralization induced by planktonic Bacillus cereus. Formation of precipitates in the presence of CaCl2 and urea was observed both during bacterial growth and in the medium devoid of bacteria and ECM (cell-free system). The pathway for polymorphic transformations of CaCO3 from the amorphous phase to vaterite and further to calcite was confirmed for the bacterium-induced mineralization and did not depend on the concentration of Ca2+ and urea. The structure of CaCO3 sediments differed when formed in cell-free and bacterial systems and varied depending on time and the medium composition. The rate of precipitation was accelerated in the presence of DNA, which had little effect on the solid phase structure in the cell-free system, while strongly affecting the structure and polymorphic composition of the precipitates in bacterial culture.