The Molecular Doping process is based on the deposition of a self-assembled layer of dopant-containing molecules over the surface of a semiconductor substrate. The dopant atoms are released inside the substrate during the successive drive-in annealing step. In the typical deposition conditions, the formation of the layer is in the order of the tens of minutes, allowing for a fast dopant source layer formation. Even if the process is well controlled and its doping efficiency already demonstrated [Nanomaterials 2021, 11, 1899. https://doi. org/10.3390/nano11081899], however the early stages are very interesting to study because they reveal the micro-and nano-features of the final self-assembled layer, not known so far. Our previous works suggest that molecular clusters form during the early nucleation phase, and they successively grow into self-assembled layers on the substrate. Little is known about the nucleation kinetics influence on the molecular clusters’ morphology and the final morphological properties of the layers. In this work, we monitor the nucleation and coalescence process, in terms of molecular clusters density, size and shape, of diethyl-propyl phosphonate on silicon at different deposition conditions through a high-resolution morphological characterization. We correlate the results to the electrical characteristics of the final doped samples identifying the role of the clusters characteristics, and how these impact the electrical properties.