In this work, the use of ZrO2 nanocoating in aluminum substrates, generated by controlled electrochemical chronoamperometry in hexafluorozirconic acid solutions (H2ZrF6·5H2O), resulted in a lower porous films than that obtained by chemical conversion coating. After the application of an epoxy coating, long-term cyclic immersion corrosion tests and scratch tests proved the superior protection of the dual system and the coating lifespan, thanks to the enhanced adhesion of ZrO2 intermediate layer and the organic coating. As zirconium-based electrolytes are considered more friendly bath if compared to that of other conversion coating processes, like chromating, phosphating or anodizing processes, the study opens new insights to the protection of structural metals in sectors such as automotive, naval and aerospace industries. The main advantages are the employment of lightweight intermediate pre-treatment (nanoscale), compared to conventional ones (microscale), and reduction of waste slurry (electrolyte bath free of additives).