The modification of octadecanethiolate self-assembled monolayers on Au and Ag by nitrogen-oxygen downstream microwave plasma with variable oxygen content (up to 1%) has been studied by synchrotron-based high-resolution X-ray photoelectron spectroscopy. The primary processes were dehydrogenation, desorption of hydrocarbon and sulfur-containing species, and the oxidation of the alkyl matrix and headgroup-substrate interface. The exact character and the rates of the plasma-induced changes were found to be dependent on the substrate and plasma composition, with the processes in the aliphatic matrix and headgroup-substrate interface being mostly decoupled. In particular, the rates of all major plasma-induced processes were found to be directly proportional to the oxygen content in the plasma, which can be, thus, considered as a measure of the plasma reactivity. Along with the character of the observed changes, exhibiting a clear dominance of the oxidative processes, this suggests that the major effect of the oxygen-nitrogen downstream microwave plasma is provided by reactive oxygen-derived species in the downstream region, viz. long-living oxygen radicals and metastable species.