X-ray diffraction, transmission electron microscopy, extended x-ray absorption fine structure spectroscopy, and x-ray photoemission spectroscopy have been used to study the structural properties of MnxGe1−x ion implanted alloys (x≃0.04) at 240 and 270°C substrate temperatures. Between 40% and 50% of the Mn atoms are found to occupy substitutional sites. No interstitial Mn atoms are found. The Mn–Ge coordination distance is 2.50(2)Å. Moreover, in the subsurface implanted layer [up to 32(2)nm depth] all the Mn atoms are effectively diluted in the Ge matrix, reaching a peak doping concentration of 7±1%.