An RF sample-processing micro-reactor that was developed as part of potential in situ exploration missions to inner- and outer-planetary bodies has been used to perform hydrolysis of a protein—lysozyme. The micro-reactor was designed to utilize aqueous solutions subjected to 60 GHz radiation at 730 mW input power to extract target organic compounds and molecular and inorganic ions as well as to hydrolyze complex polymeric materials. High performance liquid chromatography (HPLC) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) were used in the analysis of the reaction products. It was established that both the flow rate of the protein solution through the reactor (2.5–87 μL min⁻¹) and the applied head pressure (0.34–2.76 MPa) positively affect the hydrolysis reaction when exposed to RF radiation. The results of the RF micro-reactor samples were compared to those run in an analogous sample handling setup using a heat source in place of RF radiation.