Studies with overweight people are a priority in order to observe the effect of the timing of intervention on pre-obesity people. The aim was to compare different physical activity programs plus an individualized hypocaloric diet on body composition in overweight subjects. A randomized controlled clinical trial was carried out in overweight adults with no history of relevant illness. Primary outcome was total fat mass (TFM). Participants were allocated into four activity programs with equal intensity and volume of exercise for 22 weeks: strength training (S), endurance training (E), strength + endurance training (SE), and 'adhering to physical activity recommendations' (C). Participants followed a diet with 25% less energy (50%-55% carbohydrates, 30%-35% fat) measured by accelerometer. Variables were assessed at baseline and at the end of the intervention. Body composition was measured by dual-energy X-ray absorptiometry. One hundred nineteen from 205 subjects were randomized in the four exercise groups (S = 30/E = 30/SE = 30/C = 29) and 84 participants (36 men/48 women) ended the intervention (S = 19/E = 25/SE = 22/C = 18). At the end of the experiment, all groups except C increased their total physical activity (S = 1159 ± 1740; E = 1625 ± 1790; SE = 1699 ± 2516; C = 724 ± 1979 MET-min/week). Using an ANOVA-test, improvements were observed in body weight (S = -4.6 ± 4.5; E = -6.6 ± 4.6; SE = -8.5 ± 2.8; C = -6.1 ± 5.6 kg, = 0.059) and TFM (S = -4.24 ± 2.02; E = -4.74 ± 2.96; SE = -6.74 ± 3.27; C = -3.94 ± 4.18%; < 0.05). The main conclusion was that there were no adverse events. Strength and endurance training with a balanced, individualized hypocaloric diet was the most effective at reducing weight loss and fat mass in overweight subjects. Trial registration: NCT01116856.