The preservation of organic biosignatures during the Proterozoic Eon required specific taphonomic windows that could entomb organic matter to preserve amorphous kerogen and even microbial body fossils before they could be extensively degraded. Some of the best examples of such preservation are found in early diagenetic chert that formed in peritidal environments. This chert contains discrete domains of amorphous kerogen and sometimes kerogenous microbial mat structures and microbial body fossils. Our understanding of how these exquisite microfossils were preserved and the balance between organic degradation and mineral formation has remained incomplete. Here, we present new insights into organic preservation in Proterozoic peritidal environments facilitated through interactions among organic matter, cations, and silica. Organic matter from Proterozoic peritidal environments is not preserved by micro- or cryptocrystalline quartz alone. Rather, preservation includes cation-rich nanoscopic phases containing magnesium, calcium, silica, and aluminum that pre-date chert emplacement and may provide nucleation sites for silica deposition and enable further chert development. Using scanning electron microscopy and elemental mapping with energy dispersive X-ray spectroscopy, we identify cation enrichment in Proterozoic organic matter and cation-rich nanoscopic phases that pre-date chert. We pair these analyses with precipitation experiments to investigate the role of cations in the precipitation of silica from seawater. Our findings suggest that organic preservation in peritidal environments required rapid formation of nanoscopic mineral phases through the interactions of organic matter with seawater. These organic-cation interactions likely laid the initial foundation for the preservation and entombment of biosignatures, paving the way for the development of the fossiliferous chert that now contains these biosignatures and preserves a record of Proterozoic life.