Global seismic discontinuities near 410 and 660 km depth in Earth’s mantle are expressions of solid-state phase transitions. These transitions modulate thermal and material fluxes across the mantle and variations in their depth are often attributed to temperature anomalies. Here we use novel seismic array analysis of SS waves reflecting off the 410 and 660 below the Hawaiian hotspot. We find amplitude–distance trends in reflectivity that imply lateral variations in wavespeed and density contrasts across 660 for which thermodynamic modeling precludes a thermal origin. No such variations are found along the 410. The inferred 660 contrasts can be explained by mantle composition varying from average (pyrolitic) mantle beneath Hawaii to a mixture with more melt-depleted harzburgite southeast of the hotspot. Such compositional segregation was predicted, from petrological and numerical convection studies, to occur near hot deep mantle upwellings like the one often invoked to cause volcanic activity on Hawaii.