Studying the proximate mechanisms of social behaviour poses unique methodological and theoretical challenges. In a series of studies, we used pupillometry to design experimental paradigms that allow us to investigate physiological changes in the context of both children’s and chimpanzees’ social interactions. We applied these methods to study the underlying motivation of both prosocial behaviour and so-called inequity aversion. In young children, we have further included measures of positive emotions using motion sensor technology. Together, our results suggest that while specific social behaviours, such as helping, are a cross-species phenomenon among Great Apes, the underlying motivation may be distinctly different between humans and chimpanzees.