High resolution X-ray diffraction and synchrotron radiation multiple diffraction were used to investigate the structural effects induced by 5 MeV Au²⁺ ion irradiation into amorphous Fe–Si thin layers synthesized by Fe⁺ ion implantation in a Si(001) substrate. The concentration–depth profile and damage distribution induced by the Fe and Au ions were estimated by Monte-Carlo calculations (TRIM code) and were used to support the obtained experimental results. Grazing incidence X-ray diffraction and reflectivity measurements show the amorphous feature and interface quality of the as-implanted and Au-irradiated samples. Matrix and a distinct Si-distorted region contributions were detected by high resolution (004) rocking curves, as well as by Si(113) asymmetrical reciprocal space mapping patterns, for just the Au-irradiated samples. They have also shown defect distribution on the Si-distorted region interface plane. The exact multiple diffraction condition of the (1)(13) four-beam case was tailored and showed in a single ω:phi mapping, through the (1-13) coherent hybrid reflection, all previously detected effects of the Au-irradiation in the Si lattice. It is the first observation of this kind of hybrid reflection in an ion implanted and irradiated Si substrate. From the incidence (ω) and azimuthal (ϕ) angular positions measured, the Si-distorted region lattice parameters were determined along the in-plane and out-of-plane directions.