PURPOSE: This study aimed to investigate the influence of different exercise training modalities on heart rate variability (HRV) in sedentary middle-aged adults; and to study whether changes in health-related outcomes (i.e., body composition and cardiometabolic risk) are associated with those hypothetical HRV changes in sedentary middle-aged adults. METHODS: A total of 66 middle-aged adults (53.6 +/- 4.4 years old; 50% women) were enrolled in the FIT-AGEING study. We conducted a 12-week randomized controlled trial. The participants were randomly assigned to 4 groups: (a) a control group (no exercise); (b) a physical activity recommendation from the World Health Organization group (PAR); (c) a high-intensity interval training group (HIIT); and (d) a high-intensity interval training group adding whole-body electromyostimulation (HIIT + EMS). RESULTS: All exercise training modalities induced changes in HRV parameters (all P </= 0.001) without statistical differences between them (all P > 0.05). We found associations between changes in body composition and cardiometabolic risk and exercise-related changes in HRV. CONCLUSION: Our results suggest that different exercise interventions (i.e., PAR, HIIT and HIIT + EMS) induced an enhancement of HRV in sedentary middle-aged adults. Our findings support the notion that exercise-related changes in HRV are associated with changes in body composition and cardiometabolic risk after the intervention program CLINICAL TRIAL REGISTRY: NCT03334357 (ClinicalTrials.gov). November 7, 2017 retrospectively registered.