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The present work investigates the electrocatalytic performance of two different morphologies of boron doped-diamond film electrode (microcrystalline diamond - MCD, and nanocrystalline diamond - NCD) used in electrochemical oxidation for the removal of the antibiotic ciprofloxacin (CIP). A thorough study was conducted regarding the formation of the MCD and NCD films through the adjustment of methane in CH4/H2 gas mixture, and the two films were compared in terms of crystalline structure, apparent doping level, and electrochemical properties. The physicochemical results showed that the NCD film had higher sp2 carbon content and greater doping level; this contributed to improvements in its surface roughness, as well as its specific capacitance and charge transfer, which consequently enhanced its electrocatalytic activity in comparison with the MCD. The results obtained from CIP removal and mineralization assays performed in sulfate medium also showed that the NCD was more efficient than the MCD under all the current densities investigated. The effects of CIP concentration and the evolution of the final by-products, including short-chain carboxylic acids and inorganic ions, were also investigated. The electrochemical performance of the NCD was evaluated in different aqueous matrices, including chloride medium, real wastewater and simulated urine. The application of the NCD led to complete or almost complete CIP degradation, regardless of the medium employed. The kinetic constant rates obtained under the different media investigated were as follows: synthetic urine (0.0416 min−1 – R2 = 0.991)