Introduction: Domestication can lead to marked alterations in the biobehavioural profile of a species. Furthermore, during ontogeny, the individual phenotype of an animal can be shaped by the environment in important phases such as adolescence. We investigated differences in biobehavioural profiles between domestic guinea pigs and their ancestor, the wild cavy, over the course of adolescence. At this age, comparisons between the two groups have not been conducted yet. Male guinea pigs and cavies were subjected to a series of tests twice: during the early and late phase of adolescence. We analysed emotional and social behaviours as well as cortisol reactivity and testosterone levels. Results: Concerning emotional behaviour, cavies were more explorative and showed more anxiety-like behaviour in the open field test and dark-light test. They also were more risk-taking when having to jump off an elevated platform. Regarding social behaviour, cavies showed less social activity towards unfamiliar females and infants. Furthermore, while guinea pigs and cavies did not differ in basal cortisol levels, cavies showed distinctly higher and prolonged cortisol responses when exposed to an unfamiliar environment. Cavies also had lower basal testosterone titres. No substantial changes in biobehavioural profiles were revealed over the course of adolescence in both groups. Conclusions: Domestication led to a substantial shift in the biobehavioural profile of the guinea pig regarding all investigated domains in early and late adolescence. Hence, the differentiation between guinea pigs and cavies emerges early in ontogeny, well before the attainment of sexual maturity. The young individuals already show adaptations that reflect the differences between the natural habitat of cavies and the man-made housing conditions guinea pigs are exposed to. Higher levels of exploration and risk-taking and lower levels of anxiety-like behaviour are necessary for cavies in order to cope with their challenging environment. Their high cortisol reactivity can be interpreted as an energy provisioning mechanism that is needed to meet these demands. By contrast, guinea pigs are adapted to a less challenging environment with much higher population densities. Hence, their biobehavioural profile is characterised by higher levels of social activity and lower levels of exploration, risk-taking, and cortisol reactivity.