Thin films of copper-indium alloy electroplated on molybdenum substrates show different morphologies related to the substrate treatment. An ammonia treatment of the molybdenum electrode can remove a thin oxide layer from the electrode surface, changing the morphological structure of the deposit. The nucleation kinetics of copper were investigated by potentiostatic current-time transients. The deposition process involves instantaneous nucleation for untreated substrates and progressive nucleation for ammonia treated substrates, with diffusion-controlled growth of the three-dimensional nuclei. A higher nucleation density is observed for ammonia-treated molybdenum substrates. The film morphology of the copper-indium alloys can be closely related to the copper nucleation mechanism. On the untreated substrates a low nucleation density together with high adatom mobility lead to the formation of a globular structure. However, when the nucleation density is high and the nuclei are formed continuously during crystal growth, the film evolves towards a porous structure. After the selenization step the film morphology appears related to the precursor structure.