Phosphorite deposits form through phosphogenesis, a mechanism of diffusion and concentration of interstitial phosphate in sediments leading to Ca-phosphate mineral precipitation in a favorable sedimentary regime at the seafloor. Stretching along the Peruvian coast, the East Pisco Basin is known to host phosphorite beds of Miocene age. In this study, we investigate the petrographic, mineralogical and chemical composition of the Miocene phosphorite layers of the East Pisco Basin, and discuss the phosphogenetic mechanism(s) and sedimentary dynamics that led to the genesis and accumulation of P-rich deposits. Phosphorite samples were collected from layers overlaying stratigraphic unconformities within the Pisco Formation and subsequently analyzed through multiple methods: optical microscopy, XRD, XRF, SEM-EDS, EPMA, ICP-MS and LA-ICP-MS. Our results indicate that these layers consist of phosphatic clasts and nodules along with dolomite clasts, basement boulders, shark teeth, mollusk molds and vertebrate bone fragments. The P-rich clasts are mainly composed of phosphatic intraclasts and small phosphatic nodules. They occur associated with minor amounts of dolomite clasts coated by Fe-oxyhydroxides and laminites. Clasts and nodules are cemented by both early and late diagenetic cements, such as dolomite, calcite, silica, gypsum/anhydrite and baryte. Our observations suggest that the Pisco phosphorite deposits are transgressive lags laying on ravinement surfaces. They formed just below the sediment-water boundary during the early transgression phases, when the porewaters were enriched in phosphorus due to the abundance of organic-rich sediments and the microbial activity, as typical of upwelling settings. These deposits formed in shallow marine conditions, characterized by high biological productivity and low net sedimentation rates, with suboxic conditions at and beneath the sediment-water interface. The concentration of phosphate-coated clasts was then favored by a sedimentary condensation mechanism of dynamic bypassing. Overall, this study provides new insights into the genesis of phosphorite layers in the East Pisco Basin and highlights the importance of understanding the complex interplay between authigenic and sedimentological processes in the formation of these economically and geologically relevant sedimentary rocks.