In this study we demonstrate the possibility to prepare highly sensitive nanostructured electrochemical immunosensors by immobilizing the biorecognition elements on the polycarbonate (PC) surrounding the gold nanodisks in nanoelectrode ensembles (NEEs). The nanodisk electrodes act as bare electrochemical transducers in close proximity (not in direct contact) with an antigen or antibody-based biorecognition layer. Suitable soluble redox mediators shuttle electrons to/from the biorecognition layer from/to the nanoelectrodes, so exploiting the maximum advantage from the highly improved signal-to-background current ratio, typical of NEEs. In particular, horse radish peroxidase was used as the enzyme label and methylene blue as the redox mediator. Two detection schemes were tested: scheme A, based on the direct immobilization of the target protein on the PC of the NEE, and scheme B, based on the immobilisation on PC of an antibody to capture the target protein. In both case, the biorecognition process was completed by adding a primary antibody and a secondary antibody with the enzyme label. Typical target analytes were Single Chain Fragment Variable antibodies, for scheme A, and Her2-receptor, for scheme B. NEE based tests resulted much more sensitive with respect to western blot tests.