Phosphorus (P) usually occurs as microcrystalline minerals of carbonate fluorapatite (CFA) in sediments of upwellingrelated areas. The Upper Cretaceous/Paleogene marine sedimentary rocks in Morocco host the world’s largest economic reserves in phosphorus, which were deposited on the eastern passive margin of the central Atlantic Ocean. However, a full petrographic, mineralogical and geochemical characterization of the Moroccan phosphate minerals is yet to be determined. Here, we use optical and scanning electron microscopies, X-ray diffraction, and infrared spectroscopy, in combination with a microprobe analyzer to document carbonate (CO3 2− ) substitutions in CFA from two distinct phosphate basins and their possible implications for paleoenvironmental conditions. The Moroccan phosphorus-rich deposits predominantly comprise porous phosphatic peloids and coated grains with a maximum size of 500 μm, which in turn consist of high-density nano- to micron-sized rod-shaped and sphere-like crystallites. Bulk and in situ analyses reveal heterogeneous CO3 2− content in CFA at the regional- and grain-scale. Fourier transform infrared spectra indicate that CO3 2− accommodates only in the phosphate site within the fluorapatite structure, as found in other natural phosphate minerals. Bulk CO3 2− variations in CFA between phosphate basins, ranging from 1.97 to 8.24%, are likely related to depositional conditions – and thus of supersaturation with respect to CFA – during mineral formation, transport, and redeposition. Moreover, some phosphatic coated grains have revealed alternations of CO3 2− -rich and CO3 2− -poor CFA laminae, pointing out local differences in CO3 2− concentrations in sediment pore waters. Interestingly, the change in shape and diminution in size of CFA crystallites caused by high content of CFA-hosted CO3 2− could have possibly increased the intragranular porosity, highlighting an underestimated role of CO3 2− on grain morphology. Considering the higher solubility of CO3 2− -rich CFA than fluorapatite, the application of such phosphate rocks from specific Moroccan areas as rock phosphate powders may be of deep interest for long-term soil fertilization. These results further evidence the importance of studying phosphorites for economic, environmental, and scientific interests.