Repeated exposure to external stressors could lead to altered autonomic functioning, contributing to difficulties in emotion regulation and the development of mental health difficulties. This pathway is important to investigate in autistic youths who are vulnerable to develop stress-related mental health difficulties. We investigated the interplay between resting heart rate variability (HRV), fluctuations of daily affects over time (daily affective dynamics) and mental health symptoms (internalizing, externalizing and social anxiety symptoms) in 27 autistic (M_age=17.66) and 24 non-autistic (M_age=19.86) adolescents and young adults. Resting HRV was collected using a mobile electrocardiogram. Ecological Momentary Assessment assessed daily affective dynamics (affective instability and affective reactivity to stress). Mental health symptoms were assessed with questionnaires. Resting HRV did not differ significantly between the groups. HRV was not directly associated with mental health symptoms in analyses corrected for multiple comparisons, but affective reactivity to stress mediated the association between HRV and internalizing symptoms. Finally, differences emerged in the relationship between HRV and daily affective dynamics between autistic and non-autistic individuals. Our results suggest that increased stress reactivity may be a mechanism linking altered autonomic functioning to mental health difficulties, offering important insights for targeting clinical interventions.