The low energy electron induced damage in self-assembled monolayers (SAM) formed from semifluorinated alkanethiolates (SFAT) of CF3(CF2)(9)(CH2)(n)SH (F10HnSH) with different hydrocarbon chain length (n=2, 11 and 17) on polycrystalline gold has been monitored in-situ by X-ray photoelectron spectroscopy and angle resolved near edge X-ray absorption fine structure spectroscopy. All investigated SFAT SAMs exhibit qualitatively similar behavior with respect to low energy electron irradiation. Both the fluorocarbon and hydrocarbon parts and the S/Au interface are affected simultaneously. Progressive disordering of initially well-ordered, densely packed SAMs, desorption of film constituents, and chemical changes within the residual film are observed. Desorption of sulfur-containing fragments, which probably include the complete SFAT chains, was only found for F10H2S/Au. The desorbed carbon-containing fragments originate almost exclusively from the fluorocarbon part of the SFAT SAMs. Fluorine desorbs not only as a constituent of the carbon-containing fragments, but through irradiation-induced scission of C-F bonds. The accumulated chemical changes within the residual SFAT films include the complete disappearance of CF3 tail group, partial transformation of CF2 moieties into CF entities, appearance of C=C double bonds in the fluorocarbon and hydrocarbon (predominantly) parts, and transformation of the thiolate head groups into new irradiation-induced sulfur species. Some general tendencies in the reaction of SAMs toward electron-irradiation are noticed in full agreement with previous findings for conventional AT SAMs.