The Deccan Traps in west-central India constitute one of Earth's largest continental flood basalt provinces, whose eruption played a role in the Cretaceous-Paleogene extinction event. The unknown mantle structure under the Indian Ocean at the start of the Cenozoic presents a challenge for connecting the event to a deep mantle origin. We used a back-and-forth iterative method for time-reversed convection modeling, which incorporates tomography-based, present-day mantle heterogeneity to reconstruct mantle structure at the start of the Cenozoic. We show a very low-density, deep-seated upwelling that ascends beneath the Reunion hot spot at the time of the Deccan eruptions. We found a second active upwelling below the Comores hot spot that likely contributed to the region of partial melt feeding the massive eruption.