The Atlas Mountains of Morocco, an example of an intracontinental mountain belt, display only modest tectonic shortening, yet have unusually high topography. We present new evidence from receiver functions and shear-wave splitting for localized, nearly vertical offset deformation of both crust-mantle and lithosphere-asthenosphere interfaces at the flanks of the High Atlas. These offsets coincide with the locations of Jurassic-aged normal fault reactivation that led to tectonic inversion of the region during the Cenozoic. This suggests that a lithospheric-scale discontinuity is involved in orogeny. Another significant step in lithospheric thickness is inferred within the Middle Atlas. Its location corresponds to the source of regional Quaternary alkali volcanism, where the influx of melt induced by the shallow asthenosphere appears to be restricted to the lithospheric-scale fault on the northern side of the range. Inferred stretching axes from shear-wave splitting are aligned with the highest topography, suggesting along-strike asthenospheric shearing in mantle flow guided by lithospheric topography. Isostatic modeling based on these improved crustal thickness and offset estimates indicates that lithospheric thinning alone does not explain the anomalous Atlas topography. Instead, an upwelling component induced by a hot mantle anomaly is also required to support the Atlas, suggesting that the timing of uplift is contemporaneous with the recent volcanism in the Middle Atlas. These observations provide a refined understanding of intracontinental orogeny and localized volcanism.