We synthesized Au nanostructures on glass by low-energy ion irradiation of a thin Au film. The Au films, deposited on a glass substrate, were irradiated by 50 keV Si− ions with different fluences. The UV–vis absorption spectroscopy of irradiated samples indicates the surface plasmon resonance peak, which is a signature of the formation of Au nanostructures. The surface morphology of the films has been characterized by atomic force microscopy, which supports the UV–vis spectroscopy findings. The metal content or the film thickness of the samples, as measured by Rutherford backscattering spectroscopy, decreased with increasing fluence, showing sputtering by ion irradiation and tailing in the lower energy edge with irradiation, revealing recoil implantation. The formation of Au nanostructures by this method can be explained on the basis of an interplay between surface instability due to ion beam sputtering and surface diffusion.