Mind-body interventions, such as mindfulness-based stress reduction (MBSR), can improve well-being by increasing awareness and regulation of physiological and cognitive states. However, it is unclear how the practice may alter basic physiological processes in the long term and whether these changes reflect improved well-being. Using respiratory rate (RR), which may be sensitive to the effects of meditation, and 3 aspects of self-reported well-being (psychological well-being (PWB), distress, and medical symptoms), we tested pre-registered hypotheses that: (1) A more initial RR low (in a resting, non-meditative state) would be a physiological marker associated with well-being, (2) MBSR would decrease RR, and (3) training-related decreases in RR would be associated with improvement. welfare. We recruited 245 adults (age range = 18 to 65, M = 42.4): experienced meditators (n = 42) and meditation-naïve participants randomly assigned to MBSR (n = 72), active control (n = 41 ) or waiting list control. (n=66). Data were collected before randomization, after intervention (or on hold), and at long-term follow-up. Lower baseline RR was associated with lower psychological distress among long-term meditators (p= 0.03, b = 0.02, 95% CI (0.01, 0.03)), although not in non-meditators before training. MBSR decreased RR compared to waitlist (p = 0.02, Cohen’s d = − 0.41, 95% CI (− 0.78, − 0.06)), but not active control. Decrease in RR related to the decrease in medical symptoms, in all participants (p= 0.02, b = 0.57, 95% CI (0.15, 0.98)). After training, a lower RR was associated with higher PWB in the training groups compared to the waiting list (p* = 0.01, b = 0.06, 95% CI (0.02, 0 .10)), although there were no significant differences in the change in PWB between the groups. This physiological marker may indicate greater physical and/or psychological well-being in those who engage in wellness practices.