The microbial induced biomineralization of calcium carbonate using the ureolytic bacterium Sporosarcina pasteurii in the presence of trivalent europium, a substitute for trivalent actinides, was investigated by time-resolved laser-induced fluorescence spectroscopy (TRLFS) and a variety of physicochemical techniques. Results showed that the bacterial-driven hydrolysis of urea provides favorable conditions for CaCO3 precipitation and Eu3+ uptake due to subsequent increases in NH4+ and pH in the local environment. Precipitate morphologies were characteristic of biogenically formed CaCO3 and consistent with the respective mineral phase compositions. The formation of vaterite with some calcite was observed after 1 day, calcite with some vaterite after 1 week, and pure calcite after 2 weeks. The presence of organic material associated with the mineral was also identified and quantified. TRLFS was used to track the interaction and speciation of Eu3+ as a molecular probe with the mineral as a function of time. Initially, Eu3+ is incorporated into the vaterite phase, while during CaCO3 phase transformation Eu3+ speciation changes resulting in several species incorporated in the calcite phase either substituting at the Ca2+ site or in a previously unidentified, low-symmetry site. Comparison of the biogenic precipitates to an abiotic sample shows mineral origin can affect Eu3+ speciation within the mineral.