The redeposition of pristine phosphorite plays an important role in phosphorus accumulation, which created reworked phosphorite extensively on the continental shelf. This paper, using geochemical analysis combined with data from petrology and diagenesis, focuses on the reconstruction of the formation processes of the Late Cretaceous Thaniyat phosphorite deposition in northwestern Saudi Arabia, which is a part of the famous large Neo-Tethys Ocean’s phosphorite deposit. The results of our study illustrate that the phosphorites represent the reworked products from the north, close to the edge of the Neo-Tethys Ocean’s shelf, where upwelling had accreted the pristine phosphorite. The reworked phosphatic grains were redeposited near the shore in sandstone, forming sandy phosphorite and on a carbonate platform and creating calcareous phosphorite. The microscale sedimentological and geochemical information hosted in the eroded phosphorite grains indicates that the source sediment, pristine phosphorite, occurred under a fluctuating geophysical condition and in a relatively limited geochemical environment. They were physically crushed and transported landward and deposited under oxic conditions, forming the Thaniyat phosphorites. Early diagenesis in the Thaniyat phosphorite was evidenced by recrystallization of the phosphate minerals, geochemical depletion, and C and O isotope excursion.