Fractured crystalline basement reservoirs are of increasing economic interest for oil and gas exploration and subsurface fluid storage. The successful characterization of these reservoirs is commonly challenged by their structural heterogeneity, complexity in fracture distribution and flow properties at multiple scales, and the difficulty of imaging fractures in exploration seismic. We analyzed the fracture geometry and fracture diagenetic attributes in two oriented cores from the Habban Field in the Late Jurassic Sab'atayn Basin (Yemen) to evaluate the multi-phase deformation history and fracture flow pathway evolution for (hydrothermal) fluids and hydrocarbons. Analyses included petrographic and fluid inclusion analysis of fracture-filling cements, and stable sulfur isotope analyses of fracture-filling pyrite.The Paleoproterozoic basement consists of amphibolite-facies metamorphic ortho- and paragneiss cut by several phases of Neoproterozoic granitoid intrusions. The investigated lithologies in the drill cores comprise (1) epidote quartzite, (2) amphibolite, (3) monzogranite, (4) meta-arkose, and (5) quartz-feldspar porphyry. These lithologies show an inhomogeneous fracture network that is partially cemented. Ediacaran brittle-ductile deformation (D1) recognized only within a Pan-African monzogranite lead to cataclasis and porosity generating alteration. Late Jurassic – Early Cretaceous extension (D2) related to the break-up of Gondwanaland and the formation of the Sab'atayn Basin is found in all lithologies and likely resulted in pervasive quartz cementation. Late Jurassic fractures parallel to the NW-SE trending long axis of the Sab'atayn Basin are best recognized in a strongly foliated amphibolites. Cenozoic extensional fracturing (D3) reactivated older structures, which probably formed during activity of the Neoproterozoic Najd Fault System and caused multi-phased (pyrite-(saddle) dolomite-calcite) fracture cementations. The sulfur isotope compositions of pyrite with δ34S values ranging between −17.4 and + 26.4‰ vs. V-CDT reflects the variability of the fluid source during sulphide mineral formation from hydrocarbon-rich hydrothermal solutions. Fluid inclusions indicate that cementation reactions occurred in a relatively narrow temperature field between 120 °C and 140 °C, ideal for hydrocarbon maturation. Our results demonstrate the potentially complex charge history of basement reservoirs, involving multiple phases of fracture formation and cementation, and fluid charge episodes.