In continental arcs, the exposure of primitive eruptive products at the surface is typically a result of rapid magmatic transfer through the crust. As a result, the initially primitive magma experiences minimal crustal residence and thus insignificant differentiation towards more evolved products. This rapid transfer of primitive magma through thickened crust is commonly recorded from smaller, monogenetic cinder cones. Manantial Pelado (35.5° S) is a long-lived stratocone in the Southern Andean Volcanic Zone (SVZ) overlying thick continental crust (45–50 km) that produces almost exclusively mafic material. As Manantial Pelado is surrounded by extensive silicic volcanism, the study of its mafic exposure as a stratocone can be used to further understand magmatic origins of long-lived volcanic systems. Our study uses textural, geochemical, and geochronological data from lavas collected from Manantial Pelado to characterize its magmatic petrogenesis, assess the primitive nature, and explain processes in the crust within the SVZ. A geologic description of the volcano reveals a mostly monotonous eruptive history of basaltic andesites that are now accessible through glacially carved valleys. New ⁴⁰Ar/³⁹Ar dating constrains most of the volcano’s cone constructing phase to last from ~ 220 to 190 ka. At ~ 30 ka, small-volume activity and different petrography of more intermediate magmas were present reflecting a change in the volcano’s character. A combination of the whole-rock and mineral-scale data reveals that basaltic andesites at Manantial Pelado are among the most primitive magmas in the thickened crust of the SVZ. Evidence for this primitive signature consists of textural and zonation patterns in olivine, the presence of Cr-spinel in olivine cores, and elevated Fo and Ni content within olivine cores. This data combined with elemental diffusion modeling provides evidence for a primitive signature for these lavas. Intermediate Fo olivines with uniform core compositions (Fo_80–84) suggest that basaltic andesites reside in the crust in quasi-closed system environments for extended storage prior to eruption (~ 25–6000 years). Diffusive equilibration in those intermediate Fo olivines masks the primitive nature of the magmas. These results suggest that mafic magmas can have a protracted storage history in the crust that does not significantly alter their primitive bulk composition before reaching the surface. We argue that these are important processes in understanding the magmatic origin of long-lived systems and the presence of compositionally homogenous olivines at intermediate Fo content may represent cryptic evidence for recharge with primitive magmas that experienced prolonged crustal storage.