A tunable structural engineering of nanowires based on template-assisted alloying and phase segregation processes is demonstrated. The Au-Ge system, which has a low eutectic temperature and negligible solid solubility (<10(-3) atom %) of Au in Ge at low temperatures, is utilized. Depending on the Au concentration of the initial nanowires, final structures ranging from nearly periodic nanodisk patterns to core/shell and fully alloyed nanowires are produced. The formation mechanisms are discussed in detail and characterized by in situ transmission electron microscopy and energy-dispersive spectrometry analyses. Electrical measurements illustrate the metallic and semiconducting characteristics of the fully alloyed and alternating Au/Ge nanodisk structures, respectively.