While ooids have been significant components of many shallow-water carbonates throughout Earth’s history, their abiotic or biotic origin has been much debated. Herein, we evaluate ooids from five locations in the Bahamas, where ooids are actively forming, and where ooids harbor a highly diverse microbial community with capabilities for carbonate precipitation. Using scanning electron microscopy (SEM), we identify well-preserved microbial assemblages and provide compelling evidence of biogenic signatures intrinsically related to organomineralization, including extracellular polymeric substance (EPS) exudates from biofilm-forming bacteria and diatoms; imprints of EPS degradation by heterotrophic bacteria; amorphous calcium carbonate (ACC) precipitates within microdomain areas of biofilm EPS; and extracellular precipitates on bacterial cells. As revealed by nuclear magnetic resonance and SEM imaging, ACC plays a formative role in the development of aragonite crystals in ooids. Contrary to the classical nucleation theory, aragonite mineralization in ooids occurs through prenucleation of ACC, where the intimate association between ACC and EPS and microbes suggests that ACC precipitates are biomediated. These findings argue for a new conceptual model for ooid accretion that includes a biomediated ACC metastable phase.