The storage conditions of super-eruptions, particularly regarding the timescales and thermal status of their magma reservoirs, are under debate. We present cathodoluminescence images and Ti contents of quartz crystals from two super-eruptions, the ~0.78 Ma Oldest Toba Tuff (OTT) on Sunda arc and the ~0.63 Ma Lava Creek Tuff (LCT) at Yellowstone hotspot, to compare their pre-eruptive thermal evolution histories and shed light on the links between magma storage conditions and tectonic settings. The OTT quartz crystals are commonly unzoned and crystallize at temperatures <750°C with a residence time of ~100–200 kyr constrained by Ti-in-quartz diffusion chronometry, indicating a prolonged near-solidus and steady-state magma storage. In addition, the wide range of the formation time (~1000–20 000 years) of the Ti-rich, CL-bright rims of the zoned quartz crystals reveal progressive thermal maturation of the OTT magma reservoir fed by continuous magma fluxes. In contrast, the LCT quartz crystals mostly exhibit complex oscillatory zoned patterns and crystallize above the lock-up temperature with a residence time of ~1–10 kyr, indicating rapid generation of voluminous eruptible magmas through frequent magma recharge events within the LCT silicic magma reservoir. Both the OTT and the LCT magma reservoirs show heterogeneous storage features, and the differences in thermal histories between them were also observed in other super-eruptions from the Toba volcanic system and the Yellowstone Plateau Volcanic Field, which could be associated with the distinct magma supply rates feeding large magma reservoirs in continental arc and hotspot settings.