This research investigated the effects of surface fluorination on both rates of organic compound oxidation (phenol and terephthalic acid (TA)) and ClO4–formation at boron-doped diamond (BDD) film anodes at 22 °C. Different fluorination methods (i.e., electrochemical oxidation with perfluorooctanoic acid (PFOA), radio frequency plasma, and silanization) were used to incorporate fluorinated moieties on the BDD surface, which was confirmed by X-ray photoelectron spectroscopy (XPS). The silanization method was found to be the most effective fluorination method using a 1H,1H,2H,2H-perfluorodecyltrichlorosilane precursor to form a self-assembled monolayer (SAM) on the oxygenated BDD surface. The ClO4–formation decreased from rates of 0.45 ± 0.03 mmol m–2min–1during 1 mM NaClO3oxidation and 0.28 ± 0.01 mmol m–2min–1during 10 mM NaCl oxidation on the BDD electrode to below detectable levels (<0.12 μmoles m–2min–1) for the BDD electrode functionalized by a 1H,1H,2H,2H-perfluorodecyltrichlorosilane SAM. These decreases in rates corresponded to 99.94 and 99.85% decreases in selectivity for ClO4–formation during the electrolysis of 10 mM NaCl and 1 mM NaClO3electrolytes, respectively. By contrast, the oxidation rates of phenol were reduced by only 16.3% in the NaCl electrolyte and 61% in a nonreactive 0.1 M KH2PO4electrolyte. Cyclic voltammetry with Fe(CN)63–/4–and Fe3+/2+redox couples indicated that the long fluorinated chains created a blocking layer on the BDD surface that inhibited charge transfer via steric hindrance and hydrophobic effects. The surface coverages and thicknesses of the fluorinated films controlled the charge transfer rates, which was confirmed by estimates of film thicknesses using XPS and density functional theory simulations. The aliphatic silanized electrode also showed very high stability during OH•production. Perchlorate formation rates were below the detection limit (<0.12 μmoles m–2min–1) for up to 10 consecutive NaClO3oxidation experiments.