Five late Pleistocene lava domes with a combined eruptive volume of ∼40 km3 distributed over an area of ∼2000 km2 represent the waning stages of the 10–1 Ma ignimbrite flare-up in the Altiplano Puna Volcanic Complex (APVC) of the Central Andes. Zircon crystal face (on unsectioned rims) and interior (on sectioned crystals) ages (U-Th and U-Pb, respectively) for a total of 252 crystals indicate remarkably consistent zircon crystallization histories: the youngest zircon surface ages (ca. 104–83 ka) are near 40Ar/39Ar eruption ages from sanidine and biotite (ca. 120–87 ka), but a significant population of surface ages predates eruption, ranging to secular equilibrium (with U-Pb interior ages to 3.5 Ma). The essentially continuous zircon crystallization history implies protracted magma presence, which agrees with temporally invariant Ti-in-zircon model temperatures, backed by the homogeneity of indirectly temperature-dependent compositional parameters. Zircon age spectra modeled using a finite-difference thermal and mass-balance model for open-system magma evolution indicate protracted zircon production in the magma reservoirs that require time-integrated recharge rates of ∼1 × 10−3 km3/yr, corresponding to high intrusive to extrusive ratios of 75: 1. This rate is below the ∼5 × 10−3 km3/yr threshold proposed in the literature for incubating the supereruptions defining the flare-up. When accounting for the shorter durations of high versus low recharge episodes over the ∼10 m.y. lifetime of the APVC flare-up, the contributions to composite batholith formation in the shallow crust of the APVC remained broadly constant during peaks and lulls in eruptive activity. This connotes that eruptive fluxes are a poor measure for intrusive fluxes. A corollary of this interpretation is that commonly applied intrusive to extrusive ratios will severely underestimate pluton formation rates during periods of low eruptive flux.