Knowing that carbon fibre reinforced polymers are sensitive to moisture through their interphases, carbon fibres sized with Bisphenol A diglycidyl ether were fluorinated under a N2/F2 atmosphere, which confers them a hydrophobic behaviour, as highlighted by wettability measurements. Low fluorination temperatures (< 230°C) lead to a sizing perfluorination and even overfluorination without carbon fibre fluorination, while higher temperatures (> 250°C) result in a carbon lattice fluorination with a complete desizing of the fibre through decomposition, that has been evidenced through X-Ray Diffraction and Raman spectroscopy studies. For both fluorination mechanisms, 19F Nuclear Magnetic Resonance, X-Ray Photoelectron and infrared spectroscopies have been used to study the nature of fluorine bonds. Scanning Electron Microscope and Energy-Dispersive X-Ray Spectroscopy have evidenced a core–shell structure for the fluorinated fibres with a fibre degradation at the highest temperatures, also highlighted by tensile tests, Atomic Force Microscopy and Electron Paramagnetic Resonance.