Although significant progress has been made in understanding the behavior of natural nanoparticles in Earth's critical zone (i.e., surface and near-surface environment), little is known about nanoparticle stability in higher-temperature environments where they are increasingly being found. Here we report the first direct observations of the thermal behavior of natural nanoparticles at near atomic scale, revealing that their thermal stability is dependent on particle size and on the surrounding host mineral. Native Au nanoparticles (mean diameter ∼4 nm) incorporated in arsenian pyrite from refractory Au ores were observed under the transmission electron microscope during in situ heating to 650 °C. While isolated Au nanoparticles melt, with the melting point being a function of size, we show that when incorporated in arsenian pyrite, Au nanoparticles become unstable unless the nanoparticle size distribution coarsens by diffusion-driven, solid-state Ostwald ripening. This change in nanoparticle stability starts above 370 °C, setting an upper temperature and size limit for the occurrence of nanoparticulate Au in refractory sulfides. These findings not only provide new insights into the behavior of nanoparticulate Au and other metals during geological processes and throughout their metallurgical recovery from refractory ores, but also provide a new tool to define the thermal history of nanoparticle-bearing geologic and planetary materials.