Autism spectrum disorder (ASD) is associated with atypical autonomic nervous system (ANS) function. However, little is known about this relationship, while accounting for co-occurring mental health conditions (e.g. anxiety) that are also associated with ANS dysfunction. In addition, research on the ANS has typically involved physiological measurements, without using more clinically meaningful measures of ANS dysfunction, such as the self-reported frequency of ANS-related physical health symptoms. Furthermore, very little is known about ANS function in autistic adults, given that previous research has focused on ANS dysfunction in children with ASD. Addressing these gaps in the literature, we compared ANS function in adults with(out) ASD (Study 1). Although autistic adults reported greater ANS dysfunction than matched neurotypical controls, this difference was not significant after controlling for anxiety and depression. Similarly, in a large nonclinical sample (Study 2), we found that anxiety and stress mediated the relationship between autistic traits and ANS dysfunction. Together, we conclude that ANS dysfunction is not a feature of ASD per se, but instead attributable to the high levels of anxiety and stress in autistic adults. We discuss the clinical relevance of these findings for managing ANS dysfunction and other physical and mental health concerns in autistic adulthood.