Military personnel are particularly exposed to stressful events, and overexposure to stress is both physically and mentally unhealthy. While stress management programs, such as the Tactics of Optimized Potential (TOP) and Heart Coherence (HC) have been implemented, their efficiency remains to be evaluated. The objective of this randomized control trial was to evaluate the effectiveness of the two programs among a young male population of 180 military fire fighter recruits. Based on two psychological, and one physiological measurement, namely heart rate variability (HRV), we found that both TOP and HC programs significantly increased HRV. This is promising as we know that higher HRV is consistent with better health, in most cases. Moreover, the TOP program significantly reduced perceived stress and negative mood, unlike the HC program. Combining these results, we conclude that while both TOP and HC programs influence physiological measurements, only the TOP modifies psychological evaluations. Finally, we distinguished the effects of the programs on two samples characterized by their HRV level. For the low HRV group, both programs tended to increase their HRV level, while for the high HRV group neither program had a significant effect.