We present zircon geochronologic (LA-ICPMS and ID-TIMS), trace element and Hf isotopic evidence for a complex evolution of the plutonic roots of the Eocene Coroccohuayco porphyry system, southern Peru. LA-ICPMS U-Pb dating has initially been carried out to optimize grain selection for subsequent high-precision ID-TIMS dating and to characterize crustal assimilation (xenocrystic cores). This combined in-situ and whole-grain U-Pb dating of the same grains has been be further exploited to derive a robust temporal interpretation of the complex magmatic system associated with the Coroccohuayco porphyry-skarn deposit. Our data reveal that a heterogeneous gabbrodioritic complex was emplaced at ca. 40.4 Ma and was followed by a nearly 5 Ma-long magmatic lull until the emplacement of dacitic porphyry stocks and dykes associated with the mineralizing event at ca. 35.6 Ma. However, at the sample scale, zircons from the porphyries provide insight into a 2 Ma-long lived “hidden” magmatism (probably at 4-9 km paleodepth) prior to porphyry intrusion and mineralization for which no other evidence can be found on the surface today. These dates together with zircon trace element analysis and Hf isotopes argue for the development of a long-lived magmatic system dominated by amphibole fractionation with an increasing amount of crustal assimilation and the development of a large and sustained thermal anomaly. The system was probably rejuvenated at an increasing rate from 37.5 to 35.6 Ma with injection of fresh and oxidized magma from the lower crust, which caused cannibalism and remelting of proto-plutons. The porphyry intrusions at Coroccohuayco were emplaced at the peak thermal conditions of this upper crustal magma chamber, which subsequently cooled and expelled ore fluids. Zircon xenocrysts and Hf isotopes in the porphyritic rocks suggest that this large upper crustal system evolved at stratigraphic levels corresponding to Triassic sediments similar to the Mitu group that may be present below the district. Using the zircon Ce anomaly as a proxy for oxidation state of the magma through time, we show that the high oxidation state of the porphyries is not the result of upper-crustal processes but is rather controlled by magmatic processes occurring at deeper levels. Comparison of our data with available high-precision geochronologic data at other porphyry systems suggest that such deposits may form when injection rate, volume and heat of their long-lived upper crustal magmatic system reach their peaks. Theses features might be diagnostic of a productive deposit.