The sedimentary record reveals first-order changes in the locus of carbonate precipitation through time, documented in the decreasing abundance of carbonate precipitation on the seafloor. This pattern is most clearly recorded by the occurrence of seafloor carbonate crystal fans (bladed aragonite pseudomorphs neomorphosed to calcite or dolomite), which have a distinct temporal distribution, ubiquitous in Archean carbonate platforms, but declining through Proterozoic time and extremely rare in Phanerozoic basins. To understand better the potential influences on this pattern, we built a mathematical framework detailing the effects of organic matter delivery and microbial respiratory metabolisms on the carbonate chemistry of shallow sediments. Two nonunique end-member solutions emerge in which seafloor precipitation is favorable: enhanced anaerobic respiration of organic matter, and low organic matter delivery to the sediment-water interface. This analysis suggests that not all crystal fans reflect a unique set of circumstances; rather there may have been several different geobiological and sedimentary mechanisms that led to their deposition. We then applied this logical framework to better understand the petrogenesis of two distinct crystal fan occurrences—the Paleoproterozoic Beechey Formation, Northwest Territories, Canada, and the middle Ediacaran Rainstorm Member of the Johnnie Formation, Basin and Range, United States—using a combination of high-resolution petrography, micro X-ray fluorescence and wavelength dispersive spectroscopy, C isotopes, and sedimentary context to provide information on geobiological processes occurring at the sediment-water interface. Interestingly, both of these Proterozoic examples are associated with iron-rich secondary mineral assemblages, have elevated trace metal signatures, and sit within maximum flooding intervals, highlighting key commonalities in synsedimentary geobiological processes that led to seafloor carbonate precipitation.