As stress is relevant to the formation of paranoia, maladaptive behavioral and physiological stress regulation is discussed as a crucial indicator of vulnerability. This is supported by research linking psychosis to the tendency to make less use of functional and more use of dysfunctional emotion regulation strategies (ER) and with a lower vagally-mediated heart rate variability (HRV). However, it remains unclear whether ER serves as a mediator between resting-state HRV on the one hand and subjective stress levels and paranoia on the other and whether this is specific to paranoia as compared to depression. We used an experience sampling method during seven days to repeatedly assess the experience of stress, usage of ER strategies, paranoia und depression (9/day) in a sample with subclinical positive symptoms (N = 32). Resting-state HRV was measured during a 5min interval in the laboratory. Data was analyzed by multi-level models. Higher resting-state HRV was predictive of lower stress-levels and of using more functional ER strategies (reappraisal, acceptance) in daily life, but did not predict the use of dysfunctional strategies (rumination, suppression) or paranoia. The association between resting-state HRV and stress was mediated by the usage of functional ER. Less functional and more dysfunctional ER were linked to higher levels of stress, paranoia and depression. Our study highlights that deficits in ER represent a link between psychophysiological and phenomenological aspects of paranoia but also of depression. This encourages to further investigate transdiagnostic prevention and therapy programs aiming to improve ER and to increase HRV.