The aim of this study was to describe the changes in body composition, strength and sprint performance in response to an entire competitive season of football training supplemented with 2 inertial eccentric-overload training sessions a week in young male professional soccer players. Whole body and regional composition (assessed using dual-energy X-ray absorptiometry), power output in half-squat and 40-m sprinting performance were evaluated in fourteen players. The eccentric-overload training consisted of training sessions a week of 1-2 sets of 10 exercises of upper-body and core (Day 1) and lower-body (Day 2), during the entire competitive season (27 weeks). Whole body fat mass decreased (-6.3 ± 3.6%, ES = -0.99 ± 0.54) substantially while lean mass increased (2.5 ± 0.8%, ES = 0.25 ± 0.09), with some regional differences. There was a substantial increase in half-squat power output (from 3% to 14%, ES from 0.45 to 1.73) and sprint performance (from 1.1% to 1.8%, ES from -0.33 to -0.44), however performance changes were not correlated with changes in body composition. A combined soccer and eccentric-overload training program was able to promote positive changes in body composition and physical factors relevant to both on-field performance and injury prevention in elite soccer players.