Molecular Doping (MD) is a technique in which dopant-containing molecules, used as a dopant source, are deposited on top of a semiconductor and diffused inside it through a drive-in process. Every phase of the MD process represents a step onto which subsequent phases will build upon to obtain the final doped sample, so an in-depth study of each phase will improve the control on the electrical properties of the final doped samples. Hence, studying the chemical bonds forming during the deposition step between the molecules becomes an essential aspect to be studied. It is already known from the literature1 that the molecules form a self-assembled monolayer over the semiconductor, but little is known on the possible multiple layers forming on top after prolonged deposition times. To this end, we performed high-resolution morphological analyses to investigate the molecular surface coverage at different timestamps and examined the effect of the surface treatments on it. To gain deeper theoretical insight on the bonding nature, we pair these analyses with density functional theory simulations, as an extension of the previous study2, and with electrical measurements of the final doped samples. We find information on the type of chemical bonds forming between the several layers of molecules and how they impact the doping profile. This will allow for a more precise tuning of the electrical properties of MD-based devices. 1 S. Caccamo et al., Materials Science in Semiconductor Processing 42, 200-20 (2016) 2 Puglisi, RA, et al. Direct observation of single organic molecules grafted on the surface of a silicon nanowire. Sci Rep 9, 5647 (2019).