The aim of the study was to analyse interaction processes in equine-assisted therapy (EAT) sessions with ten female clients in the period of emerging adulthood with intellectual disability (ID). Heart rate (HR), heart rate variability and salivary cortisol levels have been analysed in humans and horses before, during and after a standardised therapy session as well as in a control condition. There was a trend of lower cortisol levels and higher variability and parasympathetic tone induced by horses. During challenge however, there was a significant lower HR in the horse condition. Significant correlations in heart rate between therapist, client and horse were found with stronger interaction with a familiar horse. Our findings suggest that EAT may effectively modulate stress in humans with ID. Our results further elucidate synchronisation patterns in HR highlighting the pivotal role of relationship quality and intensity as modulators of synchrony.