Carbonate mud is crucial in the global carbon cycle and serves as a key sedimentary archive for paleoclimate reconstruction. Understanding the mechanisms behind its formation is crucial for explaining long-term carbon storage, including atmospheric carbon dioxide transfer to the hydrosphere and variations in mud production over geological timescales. Various mechanisms explain carbonate mud formation in both lake and marine sediments. Using bio-physicochemical methods on deep sediments of Lake Ilay, Jura, France, we propose a model of micrite formation. Our study shows that micrite mineralization occurs in sediments due to the degradation of ooze rich in exopolymeric substances throughout the sediment core’s depth. This mineralization continues as long as exopolymeric substances are present, persisting for at least 2000 years. Cryo-Scanning electron microscope imaging reveals calcite nucleation at degraded exopolymeric substance nodes, advancing with substance degradation and calcium release. These findings provide insights into fossil carbonate mud origins and formation processes.