High-intensity exercise interventions are often promoted as a time-efficient public health intervention to combat chronic disease. However, increased physical effort and subsequent fatigue can be barriers to long-term maintenance of high-intensity exercise programs. The purpose of the present study was to determine if heart rate variability (HRV) mediated state traits related to exercise program adherence. Fifty-five healthy men and women (ages 19-35 years) used a commercially available smartphone application to monitor daily HRV status throughout a 6-week high-intensity exercise intervention. Participants reported state motivation to exercise and global physical fatigue immediately prior to each exercise session. Temporary shifts toward increased parasympathetic reactivation (p = 0.030) resulted in significant increases in daily fatigue (p < 0.001) and decreases in motivation to exercise (p = 0.028). Through modulation of exercise volume, in response to these temporary shifts in HRV, these effects were reversed (p < 0.001) via increased parasympathetic withdrawal (p = 0.018). For the first time, these data demonstrate a mediating effect of HRV on adherence-related trait states throughout a high-intensity exercise program. Applied strategies, such as appropriately timed exercise volume moderation, may be able to leverage this effect and help facilitate long-term exercise program maintenance. Novelty These data establish a link between expected shifts in HRV throughout high-intensity exercise programs with motivation to participate and physical fatigue. Modulation of training volume, in response to these shifts, can optimize adherence-related behavioral responses during high-exercise programs.