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Silicon nanowires inspire since decades a great interest for their fundamental scientific importance and their potential in new technologies. When decorated with organic molecules they form hybrid composites with applications in various fields, from sensors to life science. Specifically the diethyl 1-propylphosphonate/Si combination is considered as a promising alternative to the conventional semiconductor n-type doping methods, thanks to its solution-based processing, which is damage-free and intrinsically conformal. For these characteristics, it is a valid doping process for patterned materials and nanostructures such as the nanowires. Our joined experimental and theoretical study provides insights at atomistic level on the molecular activation, grafting and self-assembling mechanisms during the deposition process. For the first time to the best of our knowledge, by using scanning transmission electron microscopy the direct visualization of the single molecules arranged over the Si nanowire surface is reported. The results demonstrate that the molecules undergo to a sequential decomposition and self-assembling mechanism, finally forming a chemical bond with the silicon atoms. The ability to prepare well-defined molecule decorated Si nanowires opens up new opportunities for fundamental studies and nanodevice applications in diverse fields like physics, chemistry, engineering and life sciences.