Abstract. Batholith emplacements within a continental margin may bear witness of a magmatic input lasting for several million years. Consequently, the geochemical signatures of such sections are complex, and their understanding in terms of petrological processes, is crucial. The Arequipa section of the Coastal Batholith of Southern Peru was discontinuously constructed during several periods of magmatic activity, from the Jurassic to the Paleocene (200–175 Ma, and 90–60 Ma). Thermobarometric data on amphiboles indicates two main levels of emplacement at the batholith scale, the deepest between 5 and 7 km in depth and the second around 3.5 km. The present day outcropping of these different units at the same elevation argue for a large vertical movement along the Lluclla Fault System between 76 and 68 Ma. Both major/trace element contents and Nd-Sr isotopes show a large variability that is not random. The data dispersion is consistent with a two-staged evolutionary model of the magmatic arc, inspired by the MASH model: (i) an early stage dominated by hybridization and fractional crystallization processes, (ii) a late stage in which magmas were homogenized and mainly evolved by fractional crystallization. The change from one stage to another is controlled by the thermal state of the crustal arc section, especially the Deep Crustal Hot Zone.