Sports participation is one of the most popular forms of physical activity among youngsters. This study aimed to examine the changes in the estimated body composition, strength, and flexibility of adolescent boys after 12 months of soccer training compared with those of age-matched controls with non-sports participation. We assessed 137 boys (62 soccer players and 75 controls) at baseline (TM1) and 12 months later (TM2). The differences in estimated body composition, strength, and flexibility were investigated using a repeated measure analysis of variance. The analysis revealed a significant main effect of soccer training on fat mass (F = 73.503, p ≤ 0.01, η2 = 0.59) and fat-free mass (F = 39.123, p ≤ 0.01, η2 = 0.48). Over time, the soccer group decreased their fat mass and increased their fat-free mass, while the opposite results were observed for the controls. Among physical fitness tests, a substantial effect of soccer training was evidenced for the sit-up performance (F = 16.224, p ≤ 0.01, η2 = 0.32). Regarding the time factor, significant effects were noted for height and handgrip strength. No significant differences were detected for flexibility. Overall, the benefits of soccer training were exhibited by the larger improvements in fat mass, fat-free mass, sit-ups, and handgrip strength performance, underlining the important role of soccer participation during adolescence.