Generation of silicic magmas leads to emplacement of granite plutons, huge explosive volcanic eruptions and physical and chemical zoning of continental and arc crust1-7. While the time scales for silicic magma generation in the deep and middle crust are prolonged8 magma transfer into the upper crust followed by eruption is episodic and can be rapid9-12. Ages of inherited zircons and sanidines from four Miocene ignimbrites in the Central Andes indicate a gap of 4.6 Myr between the start of pluton emplacement and onset of super-eruptions, with a 1 Myr cyclicity. Here we show that inherited sanidine crystals were stored at temperatures <470oC prior to incorporation in the magma. Our observations are explained by silicic melt segregation in a middle crustal hot zone with episodic melt ascent from an unstable layer at the top of the zone with a time scale governed by the rheology of the upper crust. After thermal incubation of the growing batholith, large magma chambers formed in only a few thousand years or less by dyke transport from the hot zone melt layer. Instability and disruption of earlier plutonic rock occurred in a few decades or less just prior to or during super-eruptions.