Organic matter mineralization controls how faithfully surface ecosystems and their constituent organisms are recorded in sediments and fossils, yet many of the environmental conditions governing this process remain poorly constrained. Here, we combine chemical modeling with animal decay experiments to quantify how organic-matter decay modifies local pH and the potential for mineralization via pyritization and phosphatization. pH measurements over time reveal a characteristic trajectory: an initial acidification, followed by alkalinization, consistent with the aerobic breakdown of proteins into acidic products and their subsequent anaerobic conversion to ammonia and amines. The chemical model shows that mineralization of organic matter is favored under near-neutral pH conditions and is strongly modulated by the composition and mass of organic substrates, as well as by environmental salinity and sediment permeability. Small organisms decaying in moderately permeable marine sediments are the most likely to be completely and faithfully replicated by minerals. Together, these results provide a framework for predicting the fate of organic matter in sediments and constrain how different biotic and abiotic parameters systematically bias the fossil and sedimentary record.