This is the first study of pyrite minerals in the entire West and Central African Rift System (WCARS). Several polished organic-rich core samples from the Cretaceous Yogou Formation of the Niger (Chad) Basin located in the WCARS were investigated for their pyrite content using FE-SEM and SEM-EDS imaging techniques. An attempt was made to classify the types and provenance of the pyrites and to highlight the control of rift fractures on the oxidation and dissolution of pyrites in the region. Three major types of pyrites are present in the studied formation, including euhedral pyrite (EPy) crystals, pyrite framboids (FPy), and sunflower pyrites (SPy). A statistical analysis of 307 FPy shows that the framboids are diagenetically formed with an average diameter of 6.61 μm. SPy is present in a relatively low amount compared to framboids. The pyrites underwent a variety of diagenetic modifications, from mechanical compaction to oxidation, dissolution, and recrystallization. Unoxidized pyrites primarily contain Fe, S, and C, but oxidized pyrites also contain O, Al, and Si. There is a strong correlation between the fractures and the spatial distribution of the physicochemical alteration of the pyrite in the study. Dissolution in relatively deep-buried samples occurs mainly along fracture planes. The fractures provide a pathway for oxidants and other metal elements to reach the pyrites. The pattern of pyrite dissolution reflects the timing of fracture formation and fracture activities as a purveyor or drainage for fluids in the organic-rich samples investigated. The pyrites are associated intimately with organic matter (OM); thus, the relationship between the fracture and the pyrites' transformation is significant in the assessment of organic matter preservation at deep-burial depth.