Isotopic (210Pb, 238U‐230Th, 10Be), major and trace elements, and micromorphological and microchemical data, were used to identify recent (∼100 yrs) hydrothermal alteration of a >200 kyr sedimentary record from the flank of a seamount in the Central Indian Basin located at the edge of the 75°30′E fracture zone. Alteration effects are also reflected in 1) the depleted sedimentary organic carbon, 2) dissolution features of radiolarian skeletons, 3) the presence of altered minerals such as smectite and zeolites, and 4) distinctly different magnetic properties in the altered sediments. We interpret a predominant influence of neutral chloride type hydrothermal fluids. This is the first report of recently occurring sediment alteration by shallow circulating sub‐surface fluids along the Indian Ocean intra‐plate seamount environment.