The structure of the Pyrenean Axial Zone laterally transitions from an imbricate thrust system to an antiformal stack displaying downward facing structures in its frontal part (the Nogueras zone). We carried out a paleomagnetic study through this structural transition to better constrain thrust kinematics and better define the factors controlling the occurrence of antiformal stacks. Triassic red beds unconformably overlying the Paleozoic basement were sampled across three main thrust sheets (the Nogueras zone, the Bielsa, and the Orri thrust sheets). From 31 new sites, two meaningful magnetizations were defined, both carried by hematite: (1) the primary magnetization, that unblocks at 660–685 °C and (2) an intermediate-temperature, syn-orogenic remagnetization. Paleomagnetic data indicate variable, clockwise vertical axis rotations, with mean, thrust-scale values that range from 0 to +38°. They increase both from the base to the top of the stacked units and from west to east and display a thrust-scale directional dispersion that is higher for the lower wavelength thrusts. Results evidence that increasing thrust displacements in the upper thrusts units are a key factor for the formation of antiformal stacks showing downward facing structures. Displacement gradients in the basement are transferred to cover units and can account for important rotations such as those registered by the Mesozoic-Cenozoic units to the south of the study area.