The Upper Cretaceous-Paleogene sedimentary series of the High Atlas hosts underexplored phosphate-rich sediments and presents an excellent example of how complex interactions between various geological processes control the accumulation and distribution of phosphates. Genetically-linked phosphatic lithofacies from this series were investigated for their mineralogical and geochemical compositions with the purpose of assessing the impact of post-phosphogenesis sedimentary processes on the geochemical behavior of genetically-linked phosphatic lithofacies and understanding the distribution of chemical elements. Sampled phosphatic horizons from five representative sections along the Marrakesh High Atlas borders were investigated using optical and scanning electron microscopies (OM and SEM), X-ray diffraction (XRD), inductively coupled plasma optical emission spectroscopy (ICP-OES), and inductively coupled plasma mass spectrometry (ICP-MS) techniques. Results indicated that the studied lithofacies are composed of a mixture of phosphatic and non-phosphatic particles in variable proportions depending on the facies type. However, the phosphatic fraction is dominated by carbonate fluorapatite (CFA), showing an average CO32− content of 8.40 ± 0.37 wt%. Geochemical results revealed variations in the chemical composition of the different phosphate facies. Low-grade pristine phosphatic sediment (P2O5 < 12%wt.) can be turned by the effects of storms and bottom currents into high-grade granular phosphate beds containing up to 24 wt% P2O5. This natural enrichment is mirrored in the bulk rock by increasing P2O5 concentrations against decreasing detrital phase-associated chemical elements (K, Al, Si, and Ti). Among the investigated lithofacies, karst-filling phosphate show relatively lower uranium and cadmium contents as it experienced a polyphase evolution, including winnowing, submarine reworking, transport, and subaerial weathering, traced using some redox-sensitive proxies such as cerium and uranium. Despite this polyphase sedimentary differentiation, the apatite resisted chemical changes and preserved its original geochemical signature, specifically the rare earth elements signal that reflects oxic seawater conditions. However, the differentiation processes modified the bulk rock composition of phosphates through the preferential leaching of gangue phases (e.g., carbonates). Furthermore, these processes triggered the oxidation of organic matter and sulfides, removing some associated elements of environmental concern, such as uranium and cadmium. Conclusively, the combination of mechanical winnowing/reworking and subaerial chemical weathering is the most effective way of the natural beneficiation of phosphate, both economically and environmentally.