This study presents geochemical evidence for biogenic methane formation (methanogenesis) in the shallow sediments of the oligotrophic SE Mediterranean continental shelf at water depths between 46 and 88 m. Depth-profiles of methane concentrations and related chemical parameters such as dissolved sulfate, dissolved inorganic carbon (DIC), and the stable carbon isotope composition of DIC and methane (δ13CDIC, δ13CCH4, respectively) were measured in six sediment cores (each 4.2–5.4 m long) in order to characterize the processes that involve methane production and decomposition. All the sediment cores reached the consumption depth of the entire sulfate pool and the in-situ microbial methane production (methanogenesis) zone. Methane concentrations reached saturation levels in one of the cores, but not in the others, probably because the zone of maximum methanogenesis was at a greater depth. Although the sediments exhibit a low TOC content of ~1%, the biogenic methane formation indicates a relatively high organic carbon lability capable of sustaining all redox microbial activity potential. Anaerobic oxidation of methane (AOM) was also evident in the sulfate–methane transition zone, showing a distinct isotope signature in diffusion limited conditions.