Here we report on the fabrication and characterization of cluster-assembled nanostructured zirconia electrodes for the electrochemical detection of enzymatically produced thiocholine. Zirconia nanostructures are produced by Supersonic Cluster Beam Deposition on thin gold films. This technique enables nanoscale control of the deposited film surface morphology, providing high active surface area for electrochemical detection of the analyte, along with high double-layer capacitance and suitable charge transfer resistance of the system. The electrochemical behavior of the electrodes has been characterized in the presence of the Potassium ferricyanide/Potassium ferrocyanide redox couple and the system performance showed to be enhanced starting from a thickness of the deposited layer of 60 nm. The electrochemical response for the oxidation of an enzymatic product was assessed by means of cyclic voltammetry, electrochemical impedance spectroscopy and chronoamperometry. The nanostructured zirconia film yields a good electrochemical detection of thiocholine. The limit of detection for thiocholine under working potential of 0.810-0.820 V versus reference was found to be comprised between 0.25 μM and 1.3 μM. Nanostructured electrodes, combining gold and zirconia nanoparticles can be implemented as functional transducers in biosensing devices, for example based on Acetylcholinesterase for electrochemical detection of polluting agents.