A remarkably complex electronic order of Fe2+/Fe3+ charges, Fe2+ orbital states, and weakly metal–metal bonded Fe3 units known as trimerons, was recently discovered in stoichiometric magnetite (Fe3O4) below the 125 K Verwey transition. Here, the low temperature crystal structure of a natural magnetite from a mineral sample has been determined using the same microcrystal synchrotron X-ray diffraction method. Structure refinement demonstrates that the natural sample has the same complex electronic order as pure synthetic magnetite, with only minor reductions of orbital and trimeron distortions. Chemical analysis shows that the natural sample contains dopants such as Al, Si, Mg and Mn at comparable concentrations to extraterrestrial magnetites, for example, as reported in the Tagish Lake meteorite. Much extraterrestrial magnetite exists at temperatures below the Verwey transition and hence our study demonstrates that the low temperature phase of magnetite represents the most complex long-range electronic order known to occur naturally.