Synchrotron-based high-resolution photoelectron spectroscopy was applied to study the modification of the alkanethiol (AT) self-assembled monolayers on gold and silver substrates by nitrogen-oxygen downstream microwave plasma. Because of the low density and energy of the ionizing particles, the long-lived nitrogen and oxygen radicals provided the major impact of plasma treatment. The treatment resulted in massive damage and disordering of the initially well-ordered and chemically homogeneous AT films. The most pronounced processes are the complete (AT/Au) or partial (AT/Ag) oxidation of the pristine thiolate species, partial desorption of hydrogen and carbon-containing fragments with subsequent cross-linking within the residual hydrocarbon layer, and partial oxidation of this layer, and appearance of the nitrogen-containing entities. The plasma-treatment-induced changes in the alkyl matrix and at the S-substrate interface are only partly correlated. The rate and extent of the oxidation processes at this interface are noticeably larger for C18/Au than for C18/Ag, which suggests a stronger S-metal bond in the latter system. The results demonstrate that a smallest oxygen contamination should be avoided if one wants to perform a soft modification of thin organic layers or definite molecular entities attached to these layers through the exposure to plasma.