Crustal-scale magmatic systems act as filters between the mantle and the atmosphere, and can generate large volcanic eruptions that pose significant hazards while altering Earth’s climate. Quantifying the growth rates, magma fluxes, and duration of storage at different crustal levels is crucial for understanding such systems, but these parameters are poorly constrained due to the scarcity of exposed crustal sections. Here we present the first detailed reconstruction of magma emplacement and differentiation time scales of a complete crustal-scale igneous system exposed in the southern Alps (Ivrea-Sesia region, northern Italy) to quantify the magma fluxes and duration of transcrustal magmatism. Integrated zircon U-Pb petrochronology and numerical modeling provides unprecedented evidence that the volcanic and plutonic bodies are directly related to each other both chemically and temporally, suggesting that the entire magmatic system grew rapidly from its deepest roots to the erupted products. In the entire crustal section, zircons record 4 m.y. of magma accretion, but the bulk of the magma was emplaced within approximately 2 m.y. during an episode of enhanced magma flux from the mantle. Our results show the synchronous growth and differentiation of discrete magma bodies at various crustal levels beneath silicic caldera volcanoes and reconcile modeling and geochronological results on crustal-scale heat and mass transfer.