Batch experiments of komatiite–H2O–CO2 system with temperatures from 200 to 450°C were performed to simulate the interactions between the newly formed ultramafic crust and the proto-atmosphere on Earth before the formation of its earliest ocean. Particularly, magnetite nanocrystals were observed in the experiment carried out at 450°C that are characterized by their hexagonal platelet-like morphology and porous structure. Exactly the same set of lattice fringes on the two opposite sides of one pore suggests post-crystallization erosion. The results demonstrate that magnetite could be produced by the direct interactions between the ultramafic rocky crust and the atmosphere before the formation of the ocean on the Hadean Earth. These magnetite nanoparticles could serve as a catalyst in the synthesis of simple organic molecules during the organochemical evolution towards life.