Microwave irradiation has been used for the chemical modification of functional monolayers oil silicon surfaces. The thermal and chemical stability of these layers was tested under microwave irradiation to investigate the possibility to use this alternative heating process for the surface functionalization of self-assembled monolayers. The quality and morphology of the monolayers before and after microwave irradiation was analyzed by surface-sensitive techniques. such as Fourier transform infrared (FTIR) spectroscopy, atomic force microscopy (AFM), and contact angle measurements. As a model reaction, the 1,3-dipolar cycloaddition of organic azides and terminal acetylenes was tested for the chemical modification of functional azide monolayers. Low and high molar mass compounds modified with an acetylene group were successfully clicked onto the surfaces as confirmed by FTIR spectroscopy and AFM investigations. It could be verified that the reaction can be performed in reaction times of 5 min. and a comparison to conventional heating mechanisms allowed us to conclude that the elevated reaction temperatures result in the fast reaction process.