Objectives Although the effectiveness of high-intensity training has been widely recognized as positive in athletes, its application in a clinical context is not well established. There is enough evidence to confirm that high-intensity routines are safe and that at-risk populations, such as for overweight and obese subjects, can help from these weight loss treatments. The purpose of this study was to lead a trial to test whether manipulation of physical activity in extension to high protein diet intake would induce changes in total weight and body composition. Methods Sixty-eight healthy male volunteers were randomly assigned to one of the experimental groups: a control group with a low-level prescription of physical activity (1–4 METs), moderate physical activity group that performed 10.000 steps walking per day (5–8 METs) and intense physical activity group that trained exercises by at least 70% of VO2max three times a week (> 8 METs). All subjects followed a high-protein diet designed with a reduction of 500 kcal/day. Nutritional counseling was provided throughout the study period to help ensure dietary adherence. This intervention was delivered over twenty-four sessions as weekly one-on-one, face-to-face 30-min consultations. Results A significant reduction in body fat percentage was observed in the intense physical activity group (-20.9 ± 8.8 (CI95%: -25.6 – -16.2), p < 0.001). The change in muscle mass did not produce any significant differences between groups (p > 0.05). Concerning weight, a notable weight loss was found in those subjects who performed moderate or intense physical exercise, vs. those who did light exercise, (p < 0.001) and (p < 0.003), respectively. Conclusion our data strongly suggest that resistance training should be included, whenever possible, in any dietary treatment for improving the body composition of men with overweight or obesity.