In this paper, we consider the initial nucleation of the metal film and investigate the reactions between the precursors RuCp2/CoCp2 and a series of Si-based substrates, namely: (1) H:Si(100), ( ) NHx-terminated Si(100), (3) H:SiNx/Si(100) and (4) bare Si(100), to reveal the atomic scale reaction mechanism at the first stages of metal deposition. On a bare Si(100) surface, which we use as a reference (see Supporting Information) the mechanism involves metal-carbon bond breaking yielding an adsorbed metal atom and two adsorbed Cp rings; this reaction is exothermic with computed energy changes of -7.39eV for RuCp2 and -6.80eV for CoCp2. However, the difficulty here is twofold: firstly, obtaining a bare Si surface is not likely at typical ALD operating conditions and secondly, the removal of the adsorbed Cp rings will be limited and they persist on the surface, blocking reactive sites. On H:Si(100), RuCp2 and CoCp2 have endothermic reactions for the elimination of Cp ligands via CpH formation and desorption. After an N2/H2 plasma treatment, yielding the NHx-Si(100), the resulting NHx terminations can promote the first Cp ligand elimination for CoCp2, which is overall exothermic and has a moderate activation barrier for H transfer step.