ALCUDIA is a 230 km long, vertical incidence deep seismic reflection transect acquired in spring 2007 across the southern Central Iberian Zone (part of the pre‐Mesozoic Gondwana paleocontinent) of the Variscan Orogen of Spain. The carefully designed acquisition parameters resulted in a 20 s TWTT deep, 60–90 fold, high‐resolution seismic reflection transect. The processed image shows a weakly reflective upper crust (the scarce reflectivity matching structures identified at surface), a thick, highly reflective and laminated lower crust, and a flat Moho located at 10 s TWTT (∼30 km depth). The transect can be divided into three segments with different structural styles in the lower crust. In the central segment, the lower crust is imaged by regular, horizontal and parallel reflectors, whereas in the northern and southern segments it displays oblique reflectors interpreted as an important thrust (north) and tectonic wedging involving the mantle (south). The ALCUDIA seismic image shows that in an intracontinental orogenic crust, far from the suture zones, the upper and lower crust may react differently to shortening in different sectors, which is taken as evidence for decoupling. The interpreted structures, as deduced from surface geology and the seismic image, show that deformation was distributed homogeneously in the upper crust, whereas it was concentrated in wedge/thrust structures at specific sectors in the lower crust. The seismic image also shows the location of late Variscan faults in spatial association with the lower crustal thickened areas.