Background: The present study compared the effects of performing the lateral squat exercise in three different formats from eccentric overload training on concentric/eccentric peak/mean power and inter-limb asymmetries in young soccer players. Methods: Forty-five young male (U-17) soccer players were distributed into three groups. Two groups performed the same training volume with both legs, beginning with the weaker leg (SVW, n = 15) or with the stronger leg (SVS, n = 15). The third group executed double volume with the weaker leg and also commenced with such leg (DVW, n = 15) in the lateral squat during a 10-week period. Pre- and post-intervention metrics included concentric and eccentric peak/mean power during the lateral squat test and their corresponding asymmetries. Results: All groups improved all power variables. Concentric mean and peak power asymmetry were substantially reduced in the SVW (ES: 0.89), DVW (ES: 0.43), and in SVW (ES: 1.60). Eccentric mean and peak power asymmetry were also substantially decreased in SVW (ES: 0.81) and in DVW (ES: 0.68). Between-group analyses showed substantially better performance in concentric and eccentric variables with stronger and weaker legs in SVW and DVW groups compared with SVS. Conclusions: Those groups which started with the weaker leg showed greater both power enhancements and reductions on inter-limb asymmetries.