Marine and freshwater ooids were historically thought to form by purely physicochemical processes in turbulent environments. Recently, organomineralization has been identified as a key process for the initiation of freshwater ooid cortex formation, but the exact biochemical mechanism(s) involved and subsequent contribution to the development of the growing cortex remain unknown. Here, we show that photosynthetic microbes not only enhance early carbonate precipitation around the ooid nucleus but also control the formation of the entire cortex in freshwater ooids from Lake Geneva, Switzerland. Microbial extracellular polymeric substances are first permineralized as amorphous magnesium silicates (amMg-Si) before being calcified. An ∼5‰–6‰ depletion of 13C in ooid cortices compared to both bulk values and carbonate nuclei supports this photosynthetic microbial mechanism and argues against contributions from sulfate-reducing bacteria or methanogens. These data have significant implications for paleoenvironmental studies since photosynthetic microbes now provide an alternative to turbulent hydrodynamic conditions in the formation of freshwater ooids.