Imaging the architecture of mountain roots is required to understand the support of topography and for kinematic reconstructions at convergent plate boundaries, but is still challenging with conventional seismic imaging approaches. Here we present a three-dimensional model of both compressional and shear velocities in the lithosphere beneath the western Pyrenees (southwest Europe), obtained by full waveform inversion of teleseismic P waves. This tomographic model reveals the subduction of the Iberian crust beneath the European plate, and the European serpentinized subcontinental mantle emplaced at shallow crustal levels beneath the Mauléon basin. The rift-inherited mantle wedge acted as an indenter during the Pyrenean convergence. These new results provide compelling evidence for the role of rift-inherited structures during mountain building in Alpine-type orogens.