Recognizing animal emotions is critical to their welfare and can lead to a better relationship with humans and the environment, especially in a widespread species like the donkey, which is often prone to welfare issues. This study aims to assess the emotional response of donkeys through an operant conditioning task with two presumed different emotional contents. Specifically, a within-subject design including positive and negative conditions was conducted, collecting behavioural and physiological (heart rate variability and HRV) parameters. Facial expressions, postures, and movements were analysed by principal component analysis and behavioural diversity indexes (frequencies, activity budgets, richness, Shannon and Gini-Simpson). During the positive condition, both ears were held high and sideways (left: r = -0.793, p < 0.0001; right: r = -0.585, p = 0.011), while the ears were frontally erected (left: r = 0.924, p < 0.0001; right: r = 0.946, p < 0.0001) during the negative one. The latter was also associated with an increased tendency to walk (r = 0.709, p = 0.001), walk away (r = 0.578, p = 0.012), more frequent changes in the body position (V(Body position) = 0, p = 0.022), and greater behavioural complexity (V(Gini-Simpson Index) = 4, p = 0.027). As for HRV analysis, the root mean square of successive beat-to-beat differences (rMSSD) was significantly lower after the negative condition. These non-invasive parameters could be considered as possible indicators of donkeys\' emotional state.