Investigating the intrinsic properties of molecular complexes is crucial for understanding the influence of noncovalent interactions on fundamental chemical reactions. Moreover, specific molecular recognition between a ligand and its receptor is a highly important biological process, but little is known about the effects of ionizing radiation on ligand/receptor complexes. We have probed the processes triggered by VUV photoabsorption on isolated noncovalent complexes between the glycopeptide antibiotic vancomycin and a mimic of its receptor, by means of mass spectrometry and synchrotron radiation. In the case of protonated species, the glycosidic bond of vancomycin is cleaved with low activation energy, regardless of the molecular environment. In sharp contrast, for deprotonated species, electron photodetachment from carboxylate groups only triggers CO2 loss whereas the glycosidic bond remains intact. Importantly, we also find that the noncovalent complex survives VUV photoabsorption only when the native structure is conserved in the gas phase.