Synchrotron-based high-resolution photoelectron spectroscopy was applied to study the modification of self-assembled monolayers (SAMs) of 4'-methyl- 1, 1'-biphenyl-4-thiols (BPT) on (111) gold and silver substrates by a nitrogen-oxygen downstream microwave plasma and the attachment of acrylic acid to the plasma-modified SAMs. The plasma treatment resulted in massive damage and disordering of the BPT films, with the extent and character being noticeably different for BPT/Au and BPT/Ag. Whereas for BPT/Au a profound desorption of the entire BPT moieties and a complete defragmentation of the residual hydrocarbon part occurred, only partial desorption and oxidation took place for BPT/Ag, where even a part of intact BPT moieties survived the plasma treatment. The differences in the response of BPT/Au and BPT/Ag to the plasma treatment are related to the stronger thiolate-substrate bonds for the latter system. Taking into account that an analogous difference was also observed in alkanethiolate films, one can consider it as a general property of thiol-derived SAMs. The extent of acrylic acid attachment to the plasma-treated BPT/Ag was found to be essentially larger than that to the hydrocarbon residues in the case of BPT/Au.