The mechanism by which microwave plasma is able to modify the structure and function of proteinaceous molecules is investigated. The biomolecule cystine, a dimer aminoacid, was exposed to microwave surface wave plasma produced in reactive gases, such as oxygen and nitrogen, in different conditions. Except for the physical interactions of the charged particles with the samples and the photophysical reactions induced mostly by ultraviolet radiation, these plasmas contain reactive species which promote chemical interactions. In this study we focus on the changes of biomolecules due to neutral particles inside reactive plasmas. The results proved that the effects of neutrals and charged species are not cumulative. Moreover, it seems that the charged species inside the nitrogen plasma promote nitrogen addition while the outcome of neutral exposure is cleavage. Strong oxidation occurs for oxygen treatments, most reactive species which cause oxygen addition being the oxygen molecular ions O2+.