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Continental shelves are the major sites for organic carbon burial and sulfate reduction. Organic carbon degradation and sulfidization along continental shelves are expected to play a significant role in global carbon-sulfur-iron (C–S–Fe) cycles. Here we report sediment pore-water chemistry and iron-sulfur speciation in two short cores SSK-42/9 and 10 collected off Malvan from the seasonally hypoxic shelf region off the west coast of India (WCI) at water depths of 30 and 13 m respectively. Concentration profiles of pore-water SO42−, NH4+, DIC, ΣHS− and depth-integrated sulfate reduction rates (JSO4) suggest a variable influence of sedimentation rates, the composition of organic matter (marine and terrestrial) and anaerobic oxidation of methane (AOM) on the pore-fluid chemistry. Chromium reducible sulfur (CRS) and organic-bound sulfur (OBS) are the detectable solid-phase sulfur species in the studied sediment cores. Sulfur content and isotope ratios of chromium reducible sulfur (CRS) and organic-bound sulfur (OBS) phases produced via HS−/Sx2− pathways (sulfidization and sulfurization) show contrasting profiles in SSK42/9 and 10, apparently influenced by the availability of reactive iron, the relative significance of early and late diagenetic processes, source of OBS (detritus of marine origin and sulfurized organic molecules) and diffusion of ΣHS− produced via AOM across the SMTZ. The marked influence of AOM-driven sulfate reduction and the diffusion of isotopically enriched hydrogen sulfide across the sulfate-methane transition zone (SMTZ) is apparent from the δ34SCRS profiles in SSK-42/10. Sediment TOC/TS ratios recorded in this study are significantly less than that of average modern marine surface sediments (2.8:1) underlying oxygenated water and this is attributed to the enhanced sulfidization and burial of iron-sulfur minerals in the seasonally hypoxic regions. Since the inner shelf of WCI experiences seasonal alternation from normoxia to hypoxia which may have a profound influence on the benthic community structure, nature, and depth of bioturbation/bioirrigation, we propose that the impact of these processes need to be studied at a significantly higher resolution for better understanding C–S–Fe biogeochemical cycle.