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Objective: Numerous studies associate metabolic syndrome (MetS) with poor life quality, depression, and anxiety. Aerobic exercise training has proven its value in promoting health among subjects with MetS. We aimed to evaluate the changes in health-related quality of life (HRQOL), motivation for physical activity, and the levels of anxiety and depression in subjects with MetS after individualized aerobic training. Methods: A total of 140 subjects with MetS (53.2 ± 6.8 years, 55% female) were analyzed after the random assignment to the intervention (n = 84) or the control group (n = 56). Only the intervention group participated in the 8-week HR targeted aerobic training program, which consisted of exercises on a cycle ergometer for 30‑40 min/day, 5 days/week. In all study participants HRQOL, motivation for physical activity, anxiety and depression levels were evaluated by the Medical Outcomes Study 36-Item Short-Form Health Survey, the Exercise Motivations Inventory-2, and the Hospital Anxiety and Depression scale before and after 8 weeks. Results: After 8 weeks, self-reported physical functioning significantly increased only in the intervention group (p = 0.01). The scores of mental health-summary and role limitations due to emotional problems also improved in subjects with MetS, who participated in the aerobic training program (p < 0.001, p = 0.009, respectively). The scores for social engagement motive, enjoyment and revitalization motive, and fitness motive to exercise increased (p = 0.003, p < 0.001, p = 0.023, respectively), whereas the level of depression reduced only in the intervention group (p = 0.021). Conclusions: The 8-week individualized aerobic training had a positive effect on HRQOL, motivation for physical activity, and the level of depression in subjects with MetS.