Magnetite from hydrothermal ore deposits can contain up to tens of thousands of parts per million (ppm) of elements such as Ti, Si, V, Al, Ca, Mg, Na, which tend to either structurally incorporate into growth and sector zones or form mineral micro- to nano-sized particles. Here, we report micro- to nano-structural and chemical data of hydrothermal magnetite from the Los Colorados iron oxide–apatite deposit in Chile, where magnetite displays both types of trace element incorporation. Three generations of magnetites (X–Z) were identified with concentrations of minor and trace elements that vary significantly: SiO2, from below detection limit (bdl) to 3.1 wt%; Al2O3, 0.3–2.3 wt%; CaO, bdl–0.9 wt%; MgO, 0.02–2.5 wt%; TiO2, 0.1–0.4 wt%; MnO, 0.04–0.2 wt%; Na2O, bdl–0.4 wt%; and K2O, bdl–0.4 wt%. An exception is V2O3, which is remarkably constant, ranging from 0.3 to 0.4 wt%. Six types of crystalline nanoparticles (NPs) were identified by means of transmission electron microscopy in the trace element-rich zones, which are each a few micrometres wide: (1) diopside, (2) clinoenstatite; (3) amphibole, (4) mica, (5) ulvöspinel, and (6) Ti-rich magnetite. In addition, Al-rich nanodomains, which contain 2–3 wt% of Al, occur within a single crystal of magnetite. The accumulation of NPs in the trace element-rich zones suggest that they form owing to supersaturation from a hydrothermal fluid, followed by entrapment during continuous growth of the magnetite surface. It is also concluded that mineral NPs promote exsolution of new phases from the mineral host, otherwise preserved as structurally bound trace elements. The presence of abundant mineral NPs in magnetite points to a complex incorporation of trace elements during growth, and provides a cautionary note on the interpretation of micron-scale chemical data of magnetite.