<p>A simple electrochemical method and dip-coating method were both used to synthesize novel heterostructures based on copper oxide/bismuth molybdate (CuO/Bi₂MoO₆) thin films on fluorine-doped tin oxide (FTO) substrate. The semiconductor electrode was thoroughly characterized by XRD, photoluminescence, XPS, SEM, EDS, voltammetry and chronoamperometry. Diffuse reflectance UV–Vis was measured as well as determined the optical bandgap energies. The <i>p</i>- and <i>n</i>-type semiconductor characteristics of CuO and Bi₂MoO₆, respectively, were elucidated via Mott–Schottky analysis. This analysis also facilitated the determination of their flat-band potentials, enabling the construction of the energy band alignment consistent with an efficient direct <i>Z</i>-scheme heterostructure. A highest ciprofloxacin removal efficiency of 83.7% was achieved via photoelectrocatalytic treatment using Het, wherein singlet oxygen was identified as the predominant oxidizing species, playing a primary role in the initiation and acceleration of the ciprofloxacin molecular degradation. The ciprofloxacin degradation involves three pathways through cleavage of carbon–fluorine bonds, oxidation of the piperazine ring and the decarbonylation reactions as indicated by chromatographic analysis of the degradation products. This electrode provides valuable insights into the advancement of environmentally sustainable technologies for water treatment and pharmaceutical remediation.</p>