Transformations of gold and silver nanoparticles (AuNPs and AgNPs) impact their biological effects, behaviour and fate in the human body. Interaction of NPs with endogenous biothiols is one of the major events leading to those transformations, thus the understanding of their interplay is a prerequisite for biomedical applications of NPs. This study was conducted on a model system consisting of cysteine (CYS) or glutathione (GSH) and AgNPs or AuNPs, by combining experimental and theoretical approaches. NPs were prepared by the reduction method and their shape, size distribution, zeta potential and dissolution were determined by microscopy and spectroscopic techniques. Direct interaction of biothiols with Ag and Au was monitored during NP preparation by nuclear magnetic resonance spectroscopy, and the reaction mechanism and processes on the metal surface were determined by quantum-chemical and molecular dynamics methods. In the reaction mixture, simultaneously with the formation of nanoparticles, oxidative dimerization of biothiols occurs and disulphides bind to the nanoparticle surface. Mechanism of oxidative dimerization consists of two steps: 1) oxidation of the thiol group to sulfenic acid by reactive oxygen species, and 2) reaction of thiol with sulfenic acid involving the release of one water molecule (Ag and Au act as catalysts). Generated disulphides adsorb to the AgNP and AuNP surface through non-covalent interactions with participation from all functional groups. Binding energy calculations confirm the adsorption is spontaneous, and that disulphides bind with higher affinity compared to thiols. Thus, the final product of the interaction of metallic surfaces with thiols is the formation of disulphide-coated AgNPs and AuNPs. These findings contribute to the understanding of biotransformations of both biothiols and particles that are important for the application of nanoparticles in biomedicine.