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We report on formation of non-crystalline Fe-silicides of various stoichiometries below the amorphized surface of crystalline Si(001) after irradiation with 5 keV Fe+ ions under off-normal incidence. We examined samples prepared with ion fluences of 0.1 × 1017 and 5 × 1017 ions cm−2 exhibiting a flat and patterned surface morphology, respectively. Whereas the iron silicides are found across the whole surface of the flat sample, they are concentrated at the top of ridges at the rippled surface. A depth resolved analysis of the chemical states of Si and Fe atoms in the near surface region was performed by combining X-ray photoelectron spectroscopy and X-ray absorption spectroscopy (XAS) using synchrotron radiation. The chemical shift and the line shape of the Si 2p core levels and valence bands were measured and associated with the formation of silicide bonds of different stoichiometric composition changing from an Fe-rich silicides (Fe3Si) close to the surface into a Si-rich silicide (FeSi2) towards the inner interface to the Si(001) substrate. This finding is supported by XAS analysis at the Fe K-edge which shows changes of the chemical environment and the near order atomic coordination of the Fe atoms in the region close to surface. Because a similar Fe depth profile has been found for samples co-sputtered with Fe during Kr+ ion irradiation, our results suggest the importance of chemically bonded Fe in the surface region for the process of ripple formation.