Giant volcanic eruptions have the potential to overturn civilization. Yet, the driving mechanism and timescale over which batholithic magma reservoirs transition from non-eruptible crystal mush to mobile melt-dominated stages and our capacity to detect a pending super-eruption remain obscure. Here we show, using Sr isotope zonation in plagioclase crystals from three Andean large magnitude eruptions (Atana, Toconao and Tara ignimbrites), that eruptible magma has emerged by amalgamation of isotopically diverse crystal populations and silicic melt without large-scale reheating. In each case, crystals record large isotopic diversity in crystal cores, converging towards a common value in crystal rims that coincides with the composition of the rhyolitic carrier melt. Using diffusion chronometry, we constrain that the assembled eruptible magma has resided in the Earth crust for timescales of no more than decades to centuries for Atana and Tara, and up to several millennia for Toconao. These timescales and isotopic observations are consistent with the accumulation and destabilization of melt rich layers in crystal mush. While the prospect of capturing such melt lenses with most geophysical monitoring techniques is pessimistic, gravity modelling indicate that such structures are potentially resolvable. Our findings provoke a new assessment of the origin and hazards associated with large magnitude explosive eruptions.