Stress management interventions aim to reduce the disease risk that is heightened by work stress. Possible pathways of risk reduction include improvements in the autonomous nervous system, which is indexed by the measurement of heart rate variability (HRV). A randomized controlled trial on improving stress management skills at work was conducted to investigate the effects of intervention on HRV. A total of 174 lower management employees were randomized into either the waiting list control group (CG) or the intervention group (IG) receiving a 2-day stress management training program and another half-day booster after four and six months. In the trial, 24 h HRV was measured at baseline and after 12 months. Heart rate (HR), root mean square of successive differences (RMSSD), standard deviation of normal-to-normal intervals (SDNN), and standard deviation of the average of normal-to-normal intervals (SDANN) were calculated for 24 h and nighttime periods. Age-adjusted multilevel mixed effects linear regressions with unstructured covariance, time as a random coefficient, and time × group interaction with the according likelihood-ratio tests were calculated. The linear mixed-effect regression models showed neither group effects between IG and CG at baseline nor time effects between baseline and follow-up for SDANN (24 h), SDNN (24 h and nighttime), RMSSD (24 h and nighttime), and HR (24 h and nighttime). Nighttime SDANN significantly improved in the intervention group (z = 2.04, p = 0.041) compared to the control group. The objective stress axis measures (SDANN) showed successful stress reduction due to the training. Nighttime SDANN was strongly associated with minimum HR. Though the effects were small and only visible at night, it is highly remarkable that 3 days of intervention achieved a measurable effect considering that stress is only one of many factors that can influence HR and HRV.