The topography of the Iberian Peninsula is characterized by the presence of Variscan and Alpine orogenic belts and foreland basins, but what sets it apart from the rest of Western Europe are the large elevated flat surfaces (700 m above sea-level on average) in its central parts. The origin and support of such high average topography, whether isostatic or dynamic in nature, is a matter of intense debate. To understand Iberian topography, it is key to have a reliable image of the present-day lithospheric thermochemical structure. So far, this structure remains poorly constrained, particularly at mantle level. The goal of this paper is to derive robust estimates of the thermal, compositional and density structure of the lithosphere beneath the Iberian Peninsula from an integrated geophysical-petrological probabilistic inversion of surface wave, elevation, geoid anomaly and heat flow data. Our inversion reveals an average lithospheric thickness of 80–100 km in the Iberian Peninsula with only moderate lateral variations. The most prominent lithospheric thickness change is a steep decrease from the central to the easternmost Pyrenees. The thinnest lithosphere in our models is found below the south-eastern Mediterranean margin (<80 km), overlapping with the Neogene Tallante-Cabo de Gata volcanic fields. The present-day thermochemical structure reveals a clear imprint of the geodynamic evolution of Iberia. Lithospheric thickness and, therefore, lithospheric geotherms are to a large extent related to Alpine Cenozoic compression and extension. The western Pyrenees and Iberian chains seem to have been affected by Mesozoic rifting processes that imprinted a fertile signature into the originally more refractory Variscan Iberian lithosphere. In the Betic domain to the south, the lithospheric thermochemical structure is likely conditioned by the ongoing Alboran subduction. Except for the Mediterranean margin, where we find evidence for moderate negative dynamic topography, most of the surface elevation in Iberia can be explained by lateral density contrasts associated with variations in crustal and lithospheric thickness and lithology.