Areas of old and cold oceanic plate lack conventional volcanism and have been assumed to be devoid of submarine hydrothermal activity. However, petit-spot volcanoes are common in areas of flexure of such oceanic plates. Here, we report hydrothermal ferromanganese oxides dredged from the vicinity of a petit-spot volcano at 5.7 km water depth in an area of oceanic plate flexure east of the Japan Trench. The bulk chemical, lead isotopic and mineralogical compositions of the samples indicate their formation by low-temperature hydrothermal activity, which can be interpreted as being caused by fluid–rock interactions at <200 °C. We propose that interaction of local marine sediments with volatile-rich petit-spot magmas may produce hydrothermal fluids containing not only iron and manganese but also enough amounts of carbon dioxide and methane to have implications for the global carbon cycle. However, contemporary hydrothermal activities at petit-spot volcanoes have not been confirmed yet.