Fe-Si binary compounds have been fabricated by focused electron beam induced deposition by the alternating use of iron pentacarbonyl, Fe(CO)5, and neopentasilane, Si5H12 as precursor gases. The fabrication procedure consisted in preparing multilayer structures which were treated by low-energy electron irradiation and annealing to induce atomic species intermixing. In this way we are able to fabricate FeSi and Fe3Si binary compounds from [Fe=Si]2 and [Fe3=Si]2 multilayers, as shown by transmission electron microscopy investigations. This fabrication procedure is useful to obtain nanostructured binary alloys from precursors which compete for adsorption sites during growth and, therefore, cannot be used simultaneously.