High-resolution photoelectron spectroscopy was applied to study the modification of alkanethiolate (AT) self-assembled monolayers (SAMs) on gold and silver substrates by nitrogen-oxygen downstream microwave plasma. The dominating plasma-induced processes are the oxidation of the alkyl matrix and the thiolate headgroups and the desorption of the alkylsulfonate species. The rates and extent of these processes and the mechanism of film modification depend on the substrate and the length of the alkyl chain. The films on Ag were found to be much more resistant to degradation by the reactive plasma, which is related to stronger thiolate-metal and sulfonate-metal bonds as compared to those on An and to a partial polymerization of the alkyl matrix in AT/Ag at the initial stages of the plasma treatment. On a given substrate, the length of the aliphatic chain noticeably affects the rates and extent of the oxidation and desorption processes. The major effect stems from a two-step character of the thiolate-sulfonate transformation process, which requires both the penetration of the reactive oxygen species to the headgroup-substrate interface and the oxidation event itself. Whereas for short-chain SAMs the oxidation step is rate-determining, the process becomes diffusion-limited for the long-chain films.