The Buenavista del Cobre is a world-class porphyry Cu-Mo deposit located in the Cananea Mining District, northern Sonora, México. Using zircon U-Pb dating, we show that the Proterozoic Cananea Granite, unconformably overlain regionally by Paleozoic limestones hosting skarn deposits underlies the present-day pit. We also present new crystallization ages for host rocks of copper mineralization in the District, dating for the first time a volcanic rock of the Henrietta Formation at 186.8 ± 1.1/3.0 Ma and the El Torre Syenite at 176.3 ± 1.1/2.9 Ma. Zircon U-Pb dating of the different porphyritic bodies reveals that the magmatic activity at Buenavista del Cobre lasted at least 4 Myr, from 59.7 ± 0.5/1.1 Ma to 56.1 ± 0.2/0.9 Ma. The deposit is composed by several porphyry intrusions referred to as “ore-rich” and “ore-poor” based on their individual metal contributions, which provides the opportunity to study the origin and processes enhancing magma fertility in an individual deposit. Combining our new geochronological dataset with geochemistry of apatite from the different porphyries allows us to propose a new petrogenetic model for the Buenavista del Cobre deposit. As the apatite Eu and Ce anomalies overlap with no clear difference between the ore-rich and ore-poor intrusions, we propose that the magmatic oxidation states of the magmas were similar. However, differences in apatite REE signatures, as well as variations in apatite Sr compositions between the two groups suggest that fractional crystallization processes in the parental magma influence the fertility of the porphyries. Additionally, apatite Cl contents of ore-rich porphyry intrusions are higher (>0.4 wt%) than the ore-poor intrusions (<0.2 wt%), suggesting an important role of the initial Cl content of the magmas in the mineralization process. These observations give new insights on the petrogenetic processes at origin of porphyry magma fertility. We propose that the evolution of the parental melt by fractional crystallization of hydrous minerals (hornblende) at upper crustal levels induced low H2O content of the residual magma, resulting in the formation of ore-poor porphyries. In contrast, we suggest that fractionation of anhydrous minerals (plagioclase) increased the H2O content in the residual melt, leading to the formation of ore-rich porphyries. Our new data allow us to propose an original genetic model for the Buenavista del Cobre deposit, which involves two cycles of supply, cooling and partial crystallization. This contribution shows that petrogenetic processes controlling porphyry copper magmas fertility are recorded in the composition of apatite at the deposit scale and highlights the importance of considering apatite geochemistry as an exploration tool.