The Indian Ocean is warming rapidly, with widespread effects on regional weather and global climate. Sea-surface temperature records indicate this warming trend extends back to the beginning of the 20th century, however the lack of a similarly long instrumental record of interior ocean temperatures leaves uncertainty around the subsurface trends. Here we utilize unique temperature observations from three historical German oceanographic expeditions of the late 19th and early 20th centuries: SMS Gazelle (1874–1876), Valdivia (1898–1899), and SMS Planet (1906–1907). These observations reveal a mean 20th century ocean warming that extends over the upper 750 m, and a spatial pattern of subsurface warming and cooling consistent with a 1°–2° southward shift of the southern subtropical gyre. These interior changes occurred largely over the last half of the 20th century, providing observational evidence for the acceleration of a multidecadal trend in subsurface Indian Ocean temperature.