The current literature has shown how working on coordination and agility produces effects on specific aspects in team sports. The purpose of this study was to examine the effects of a ten-week coordination training program applied to soccer on different tests that evaluate speed (30 m speed test), agility (Illinois Agility Test (IAT)) and lower body strength (countermovement jump (CMJ)). Forty U16 male soccer players from two nonprofessional teams (twenty in the control group (CG) (aged = 14.70 ± 0.47, body weight = 60.15 ± 8.07 kg, height = 1.71 ± 0.06 m) and twenty in the experimental group (EG) (aged = 14.50 ± 0.51, body weight = 58.08 ± 9.78 kg, height = 1.69 ± 0.06 m)) performed a combined coordination and agility program during 10 min every training day (3 days a week) for 10 weeks. The results of this study showed that coordination training produced adaptations in the power (CMJ of EG (p = 0.001)) and agility capacities (IAT of EG (p = 0.002)) of young soccer players, but not on speed performance at longer distances (CG, p = 0.20 and EG, p = 0.09). Despite the benefits of the training program, a combination of training methods that includes power, agility, speed, and strength can enhance such improvements.