The Pyrenees have undergone complex geodynamic evolution starting with experiencing significant tectonic events during the Variscan Orogeny, followed by the intrusion of large granitic complexes during the late Variscan stage, then the collision between the Iberian and European plates during the Alpine Orogeny, and finally, Mesozoic extension. Despite extensive studies and the application of various geophysical methods (two-dimensional seismic reflection data, gravity, and long period magnetotellurics) to investigate the Pyrenean structure, there are still fundamental questions regarding its basement and cover architecture. Specifically, the geometry at depth of significant bodies such as the Late Variscan intrusive granites and Triassic evaporitic accumulations, remains unclear. To better understand these issues, we have conducted joint magnetotelluric and gravity surveys along a 60-km-long transect, spanning the boundary between the Axial and South Pyrenean Zones. Our final geological interpretation shows that the La Maladeta batholith consists of two distinct granitic bodies related to different intrusive pulses. In addition, we identify important Triassic evaporitic accumulations at depth. This work shows the high potential of integrating two geophysical models for understanding the geological evolution of structurally complex areas. The magnetotelluric and gravity data are complementary, with each dataset providing a different resolution for investigating the basement and cover architecture of the Pyrenees. These resolutions depend on the varied petrophysical properties of the rocks involved, including water content and deformation grade.