The anaerobic oxidation of methane, a key geochemical process that is involved in the cycling of sulfate and iron (oxyhydr)oxides in marine sediments, results in the formation of iron sulfides. Although ferrimagnetic iron sulfides have been identified in seepage systems, the link between iron migration and sediment magnetic properties remains poorly understood. Here, we investigate two cores from the Sea of Marmara to evaluate biogeochemical iron cycling and iron sulfide mineralogy in gas hydrate-bearing sediments. Magnetic analyses indicate the presence of greigite and pyrrhotite in a core from a hydrate-rich site with a high hydrocarbon flux, which contrasts with a lack of these minerals in a core characterized by only mild seepage. This is supported by the results of rock magnetic and scanning electron microscope analyses of the sediments. The presence of authigenic greigite is critical for assessing local redox records and together with the occurrence of monoclinic pyrrhotite may suggest specific diagenetic processes in gas hydrate environments. Our analysis demonstrates the usefulness of these ferrimagnetic minerals, with a high saturation isothermal remanent magnetization to magnetic susceptibility ratio (SIRM/χ > 15 kAm−1) and a high index of hysteresis parameters (DJH > 0.2) indicative of magnetic mineralogy changes, for evaluating variability in the intensity of seepage fluxes and for estimating gas hydrate distributions.