Introduction. Physical activity is vital for preventing and managing lifestyle-related diseases, which pose significant health and socio-economic challenges. This study aimed to evaluate the effects of a six-month supervised physical activity program on health risk factors and body composition in middle-aged individuals with overweight or obesity. Methods. The study involved 166 men and women aged 30 to 65 years, with a body mass index (BMI) ranging from 26 to 35 and moderate to severe health risks. Participants of the study were engaged in a six-month physical activity training program designed in accordance with World Health Organization guidelines. Comprehensive assessments were performed at baseline and after the intervention, including measurements of various anthropometric and body composition parameters, as well as evaluations of functional performance. Fitness tests were also conducted to assess participants’ physical capacity and to monitor improvements throughout the training period. Results. Baseline measures of body mass composition and age demonstrated a strong positive correlation with visceral fat rating (VFR) in both men (r = 0.364, p < 0.001) and women (r = 0.420, p = 0.002). Following the six-month training program, participants exhibited an average improvement of 30% (p < 0.001) in their Cooper endurance test results. The physical activity intervention positively impacted body mass index (BMI) and various body composition metrics, including fat mass, VFR, and muscle mass, across all participants and most subgroups (gender, BMI, and age). In males, training at higher maximum heart rate (HRmax) zones significantly contributed to a reduction in the percentage of fat mass (80–89% HRmax) and an increase in the percentage of muscle mass (70–79% and 80–89% HRmax). Conclusions. The study indicates that a six-month supervised physical activity program significantly improves health risk factors and body composition (visceral fat reduction and improvement in percent of fat and muscle mass) among middle-aged individuals with overweight or obesity. Therefore, we advocate for the integration of structured physical activity interventions into healthcare practices to effectively enhance health outcomes in this population.