We studied the role of a minor fraction of oxygen in nitrogen and argon downstream microwave plasma in view of plasma-processing of ultrathin organic films -self-assembled monolayers (SAMs). As test systems we used SAMs of alkanethiolates on gold substrate. The plasma-induced processes in the films, including their chemical modification, oxidation, and partial decomposition, were monitored in detail. These processes could be directly correlated with the presence of reactive, oxygen-derived species in the plasma. The major plasma-induced processes could be well described by the first order kinetics; the respective reaction rates were also derived.