Microsedimentary structures referred to as nanobacteria-like particles were described from modern carbonate environments, where they form in close spatial association with sulfate-reducing bacteria (SRB). However, the exact mechanism of their formation, as well as their paleontological significance, remains controversial. Here we report on an investigation of microbe-mineral interactions in experimentally produced carbonate globules. The experiments were carried out under anoxic conditions at 30 °C with Desulfovibrio brasiliensis, a SRB known to mediate dolomite formation. We observed that extracellular polymeric substances (EPS) secreted by the microbial community play a key role in the mineralization process. Nanobacteria-like particles represent the early stage of carbonate nucleation within the EPS, which progressively evolve to larger globules displaying a grainy texture. We excluded the possibilities that these structures are fossils of nanobacteria, dissolution surfaces, or artifacts created during sample preparation. D. brasiliensis cells are predominantly located outside of the EPS aggregates where mineral growth takes place. As a result, they remain mobile and are rarely entombed within the mineral. This self-preservation behavior may not be limited to D. brasiliensis. Other microbes may produce, or may have produced during the geological past, biogenic minerals through a similar process. Mineralization within EPS explains why microbial relics are not necessarily present in biogenic carbonates.