CoNi and Pt-CoNi magnetic layers on indium-tin oxide (ITO) substrates modified by an alkanethiol self-assembled monolayer (SAM) have been electrochemically obtained as an initial stage to prepare semiconducting layer-SAM-magnetic layer hybrid structures. The best conditions to obtain the maximum compactness of adsorbed layers of dodecanethiol (C12-SH) on ITO substrate have been studied using contact angle, AFM, XPS and electrochemical tests. The electrochemical characterization (electrochemical probe or voltammetric response in blank solutions) is fundamental to ensure the maximum blocking of the substrate. Although the electrodeposition process on the SAM-modified ITO substrate is very slow if the blocking of the surface is significant, non-cracked metallic layers of CoNi, with or without a previously electrodeposited seed-layer of platinum, have been obtained by optimizing the deposition potentials. Initial nucleation is expected to take place at the pinhole defects of the C12-SH SAM, followed by a mushroom-like growth regime through the SAM interface that allows the formation of a continuous metallic layer electrically connected to the ITO surface. Due to the potential of the methodology, the preparation of patterned metallic deposits on ITO substrate using SAMs with different coverage as templates is feasible.