The Heart Rate Variability (HRV) is regularly associated with depression and trait emotion regulation. However, the interaction between HRV and emotional disturbances is still debated. Only a few studies indicate that HRV moderates the effect of personality traits involved in psychopathological disorders. Since the regulation of emotions is a transdiagnostic factor for most psychological disorders, this study aimed to explore whether HRV moderates the relationship between trait emotion dysregulation and depressive symptoms. We collected data from 148 participants via online questionnaires and HRV measurements at rest. Results show for the 114 female remaining in the study that whereas high emotion regulation difficulties led to higher depressive symptoms severity when resting HRV is low, depressive symptoms remain stable in the same condition but when resting HRV is high. Overall, high resting HRV appears to dampen the consequences of trait emotion regulation difficulties. Further studies are needed to confirm this result, but this suggests that usual response tendencies could be overcome by deactivating or inhibitory processes such as those implied in cognitive flexibility reflected through HRV, according to the neurovisceral integration model.