The isoinertial training method owes its efficacy to an accommodated resistance and optimal individualized eccentric overload. The aim of this study was to assess the effects of a 6-week isoinertial eccentric-overload training program - using a flywheel inertial device during the execution of specific soccer exercises - on explosive and reactive strength, sprint ability, change of direction (COD) performance and soccer shooting precision. Thirty-four junior soccer players were randomly assigned to a plyometric training group (PT) (n = 16, aged 13.36 ± 0.80), which underwent a six-week traditional soccer training program, and a flywheel eccentric overload group (FEO) (n = 18, aged 13.21 ± 1.21), which received additional training consisting of two inertial eccentric-overload training sessions per week. Pre and post intervention tests were carried out to assess explosive and reactive strength, sprint ability, COD ability, agility using the Y-agility test (YT) and soccer shooting precision. The FEO showed significantly higher values than the PT in squat jump height (SJh) (p = 0.01), drop jump height (DJh) (p = 0.003), 7 repeated hop test heights (p = 0.001), the Illinois test (ILL) (p = 0.001), and the Loughborough Soccer Shooting Test (SHOT) (p = 0.02). Finally, the FEO showed significant between-group differences in DJh (p = 0.007), ILL (p = 0.0002), YT (p = 0.002), a linear sprint test (SPRINT) (p = 0.001), and SHOT (p = 0.003). These results confirmed the positive effect of isoinertial training. The use of an isoinertial device to overload multidirectional movements in specific sport conditions leads to greater performance improvements than conventional soccer training. The absence of knowledge of the eccentric overload applied by the isoinertial device, which is different in any exercise repetition, may stimulate the athlete’s neural adaptations, improving their soccer skills and in particular their soccer shooting precision.