The Mont-Louis-Andorra granodiorite pluton, Eastern Pyrenees (France, Andorra and Spain) was the subject of a thorough study of its internal structures, principally the measurement of the anisotropy of its magnetic susceptibility and the classification of its microstructures. Regularly spaced sampling (281 sites) allowed the precise mapping of the susceptibility magnitudes, consistent with mapped rock types. The magnetic structures fall into two distinct families which occur in separate parts of the pluton and have different microstructures. Family I is observed almost everywhere and has close to horizontal lineations, remarkably constant in NE–SW azimuth. Magmatic to submagmatic microstructures characterize these rocks. In contrast, family II is confined within NW–SE-trending corridors, where moderate to steep NW-plunges of the lineations are recorded, and subsolidus microstructures are observed. Magnetic structures of family I are argued to equate with the kinematic framework of the deforming magma during its emplacement. Family II structures represent a late to post-consolidation reworking, and therefore record a second stage of deformation in the pluton. It is concluded that magma emplacement was related to a NE–SW-trending strike-slip and/or thrust fault system, coeval with the SW-verging thrust episode documented in the Pyrenees. The second stage corresponds to dextral shear movements with a thrust component on NW–SE-striking planes. Corridors containing family II structures are shear zones responsible for dissection of the massif into three blocks, the eastern block representing the former base, and the western block the top of the pluton. Restoration of the pluton's shape along these corridors demonstrates the importance of the early Variscan NE-SW kinematic direction. Because the family II structures that form shear zones affecting the pluton have similar orientation and kinematics as the compressive, steep main-phase of deformation ubiquitous in the Pyrenees, the pluton of Mont-Louis–Andorra was probably emplaced before this main-phase of deformation.