Emotion regulation (ER) is vital for healthy adaptation and influences how individuals respond to and recover from stress. We investigated whether ER improves cardiovascular, neuroendocrine and psychological stress responses, while taking into account the moderating role of habitual ER tendencies. Eighty-six women applied either cognitive reappraisal or expressive suppression (vs. control) while undergoing a stressor. Reappraisal decreased heart rate variability (HRV) during stress, but also initiated a stronger post-stress HRV-recovery relative to suppression. This reappraisal-induced cardiac-vagal-flexibility was particularly observed in habitual reappraisers. Furthermore, the reappraisal group reported enhanced positive affect, whereas the suppression group experienced more unpleasantness and expressed higher cortisol levels than controls. Heightened cortisol reactivity was also found in the reappraisal group, but only for individuals scoring low or mean on trait reappraisal. These results provide preliminary evidence that reappraisal fosters psychophysiological adaptation in response to stress, but also suggest that ER-strategy-efficacy critically depends on its habitual use.