Phosphorites are significant geological deposits that serve as key archives of past marine productivity, biogeochemical cycling, and sedimentary processes, as well as critical reservoirs of phosphorus, an essential element for global agriculture. Phosphorite deposition occurs under specific environmental settings, which allows for investigation of the interactions between microbial activity, organic matter (OM) preservation, and phosphate mineralization. This study examines the organic petrography of the Late Cretaceous Mishash Formation in southern Israel, using 37 samples from two synclines (Rotem and Zin) to classify three organofacies reflecting different diagenetic and environmental conditions. Organofacies 1, associated with OM content (1 wt.% to 7 wt.%) and significant microbial activity, likely formed under reducing conditions, followed by transition to early diagenesis in more oxic environments. In organofacies 1, degradation is demonstrated by high oxygen index (OI) and low hydrogen index (HI) values, along with evidence of bone-boring microbial activity and oxidized sulfides. Organofacies 2 shows little to no OM in the matrix (<0.7 wt.%); the minor OM that is present is armored by a coating of phosphate mineralization. The very low organic content appears to represent an extreme case of oxidative degradation. In contrast, organofacies 3, with higher OM content (2 wt.% to 25 wt.%), is characterized by a thick microbial mat laminae and in situ development of solid bitumen (a solid petroleum), suggesting preservation under reducing conditions with minimal alteration. Geochemical data reinforce these petrographic findings, showing strong correlations between OM and trace metals (Cu, Ni, Cd, Cr, Zn) in organofacies 3, but weaker correlations in organofacies 1, where oxidation depletes OM more than trace metals. This study highlights the role of varying redox conditions and microbial activity in shaping the diagenetic history of OM in phosphorites, providing valuable insights into the mechanisms of phosphorite formation and OM preservation.