In the Agly Massif (Pyrenees), two Variscan plutons, the Saint-Arnac pluton and the Ansignan charnockite, intrude different levels of a c. 10 km thick crustal section. The Saint-Arnac pluton intrudes through upper crustal rocks and the Ansignan charnockite cuts mid-crustal country-rocks. A structural study of these plutons based on the anisotropy of magnetic susceptibility technique, combined with a kinematic study of the country-rocks, shows that the structures and emplacement modes of the plutons are compatible with those of the other plutons of the Pyrenees emplaced during the D2 transpressive phase. U–Pb dating on zircons from the Saint-Arnac pluton yields a 308.3 ± 1.2 Ma age for a diorite and a 303.6 ± 4.7 Ma age for a granodiorite. The charnockite was previously dated at 315 Ma. The emplacement ages of these two intrusions are thus separated by at least 5 Ma. First, numerous sills and laccoliths, such as the Ansignan laccolith, were injected in the middle crust, and this induced heating and thickening. Subsequently, the large Saint-Arnac pluton was injected in the upper crust at the beginning of formation of a gneissic dome.