To the best of our knowledge, this study describes the first successful implementation of SERS spectroscopy to investigate the dynamic exchange of isotopologues of a thiol compound (cysteine) bound to a metal surface (AgNP). Cysteine was chosen because it can be used to anchor peptides onto the surface of noble metals facilitating the surface modification . Using the isotopically labeled SERS we detected a manifestation of not described earlier phase transition within L-Cys monolayer. We argue that through this novel investigative approach utilizing the high structural and conformational sensitivity of SERS and the straightforward thermodynamics of isotopologue exchange, one may obtain profound insights into the dynamic processes taking place within metal-anchored molecular layers. This knowledge can be further exploited across an extensive range of applications employing monolayer-modified metal nanoparticles, including heterofunctionalized systems.