<p>Self-regulation, self-efficacy, and motivation are critical correlates for exercise maintenance and play a significant role in sustaining a physically active lifestyle. Vitality and fatigue, recognized as unipolar affective states, also impact these processes by influencing exercise-induced affective responses and action initiation. This ambulatory assessment study investigates how exercise-related self-efficacy and motivation, as well as daily morning fatigue and vitality, effect cardiac activity (heart period and vagally mediated heart rate variability (vmHRV)) measured every morning in response to running. Over 8 weeks, 18 young healthy women new to running followed either a prescribed or self-determined intensity intervention. Results from multilevel analyses revealed that individuals with autonomy in choosing their running intensity exhibited increased vmHRV compared to the prescribed-intensity group. The effect vanished when predicting heart period, indicating a mediating role for parasympathetic nervous system activity concerning vmHRV. Higher self-efficacy was associated with elevated vmHRV with stable effects upon controlling for heart period. Direct effects of running, morning vitality, fatigue, or motivation on cardiac activity were not detected. The results of this study suggest that interventions promoting physical activity should enhance feelings of competence and allow self-determination to achieve activity goals. The promotion of autonomy in exercise intensity and fostering self-efficacy may support self-regulation, which could be reflected in improved morning vmHRV. These strategies have the potential to result in more effective and sustainable physical activity behaviors, thereby contributing to enhanced overall health outcomes.</p>