We investigate the mode of compensation, emplacement history and deep density structure of the Ninety-East Ridge (Indian Ocean) using spectral analyses and forward modeling of satellite gravity and bathymetry data. We find that the northern (0–10°N) and the southern (20–30°S) parts of the ridge are flexurally compensated with an effective elastic thickness >15 km, whereas the central part (0–20°S) is locally compensated. Furthermore, we find that for a part of central block (10–20°S, over Osborn Knoll) the compensation depth is unreasonably very high (30–40 km). Therefore we favor a model with subsurface loading and interpret this to be due to underplating of mafic material at the base of the crust, a hypothesis that is supported by seismic results and direct modeling of gravity data along some profiles. These results suggest that the northern and southern parts of Ninety-East Ridge were emplaced off to a ridge axis compared to the central one, which might have been emplaced on or near a spreading center. Locally compensated large topography, thick underplated crust in the central part (near Osborn Knoll), might result from an interaction of a hot spot with the extinct Wharton spreading ridge.