A common strategy to enhance the fibre-to-matrix adhesion of carbon fibres is to increase the surface polarity using extensive and harsh oxidation techniques. In this work, we use a novel and scalable strategy to significantly increase the hydrophobicity of carbon fibres without any sacrifice in the fibres' physical properties and demonstrate simultaneous increases to the fibre-to-matrix adhesion (59-216%). These findings contradict the commonly accepted paradigm of high fibre polarity correlating to increased interfacial adhesion. We demonstrate the ability to covalently modify the surface of carbon fibres through electrochemical reduction of nitroaryldiazonium salts to generate perfluorinated alkyl radicals. Surface modification was confirmed by XPS, ATRIR, and TEM. The surfaces produced are highly hydrophobic, though this may be mitigated through the reduction of nitro groups to amines, or increased through the accumulative effects of perfluoroalkyl chains and nitro groups (WCA ranges from 99.9 AE 0.4 up to 135.5 AE 0.2 , versus pristine fibre 98.4 AE 0.6). Hydrophobic fibres functionalized only with perfluoroalkyl groups were stable to both acidic (pH 1) and basic (pH 12) environments. All surface chemistries demonstrated comparable or improved interfacial shear strength and these results correlated well with calculated values of interfacial shear stress, determined via molecular dynamics simulations.