Seafloor massive sulfide (SMS) deposits in different geological settings can have variable magnetic mineralogy, but the mechanism and implications of their spatiotemporal diversity are poorly understood. Based on seabed shallow drilling and surficial sampling of the Yuhuang hydrothermal field, Southwest Indian Ridge, we investigate here whether ubiquitous oxidative weathering affects the magnetic properties of SMS deposits. Microscopic observation and ferrous iron concentrations reveal that seafloor SMS deposits are extensively oxidized; subseafloor SMS deposits are relatively fresh, but oxidation initiates immediately after sample recovery. Negative frequency dependence of magnetic susceptibility likely due to measurement eddy currents is observed for fresh samples but not for oxidized ones, which suggests that oxidative weathering reduces the electromagnetic detectability of SMS deposits in geophysical investigations. Pyrrhotite (and probably other magnetic iron sulfide minerals), magnetite, and hematite are recognized as dominating magnetic (ferromagnetic, sensu lato) minerals in SMS deposits. Electron and quantum diamond microscope observations reveal pyrrhotite mineralization from high‐temperature reducing hydrothermal fluids, while iron‐oxides are mostly oxidation products of primary sulfides. Oxidative weathering modifies paleomagnetic records of SMS deposits. Bulk magnetic parameters vary systematically with enhanced oxidation degree. Temperature‐dependent magnetic measurements are useful tools for distinguishing the oxidation state of SMS deposits. Overall, these findings explain magnetic mineral variability in SMS deposits, linking mineral magnetic properties with seafloor geophysical investigations. Mineral magnetism can also be a redox state proxy for tracing natural and artificial environmental fluctuations in seafloor hydrothermal fields, inspiring novel interdisciplinary research to understand interactions in the dynamic Earth System.