Mount Merapi is one of Indonesia’s and the world’s most hazardous volcanoes. Existing constraints on the location and the crystallization conditions of its pre-eruptive magma reservoir based on mineral and glass thermobarometry and geophysical surveys are inconclusive, yet of immediate importance for future hazard mitigation. Here, we use two series of phase equilibrium experiments to quantify the conditions of pre-eruptive magma storage and magma recharge in Merapi’s upper-crustal reservoir: (1) to characterize crystallization at total equilibrium conditions; (2) to characterize crystallization at local equilibrium conditions between crystal rims and host melt. We demonstrate that this experimental approach can constrain pre-eruptive crystallization conditions and their variation in crystal-rich, mixed magma systems, such as that of Merapi, for which standard crystallization experiments and mineral thermobarometry fail. In agreement with geophysical estimates, we infer that Mount Merapi’s pre-eruptive reservoir partially crystallizes at ≥100–200 ± 75 MPa and thus at relatively shallow depths of c. ≥4·5 to ∼9 km. Magmas are stored at ≥925–950 ± 25°C with a melt H2O content of ∼3–4 wt % and a vapour phase with an XH2O [H2O/(H2O + CO2)] of ∼0·5–0·6 ± 0·1. Pre-eruptive recharge magmas, in contrast, have a temperature >950 to <1000°C, a higher melt H2O content of ∼4–5 wt % and a vapour phase with a higher XH2O of ∼0·8 ± 0·1. We hypothesize that these variations in melt H2O content and vapour XH2O between resident and pre-eruptive recharge magmas relate to variable degrees of open-system degassing of magma parcels en route into the reservoir rather than to variations in volatile fluxing of the stored magmas.