This study examined the influence of biological maturation on the physical performance of highly skilled U-14 – U-17 male soccer players, specifically focusing on sprinting, jumping, and aerobic capacity. Sixtyseven players from a professional academy in Portugal participated in two seasons (2021–2023). Maturation was assessed at six time points, and players were categorized into pre- and circa-peak height velocity (PHV) and post-PHV groups. Owing to the small pre-PHV sample size (n = 4), these were combined with the circa-PHV group for the analysis. Key physical attributes were measured, and maturity was assessed using the predicted percentage of adult height. Mixed-effects models indicated that chronological age significantly influenced physical performance, with older players demonstrating a superior change in direction speed (p < 0.001) and sprint performance (p < 0.001), whereas maturity status had no additional effect. Maturity status interacted with age in the jumping height test (p = 0.001), with post-PHV players showing greater improvement. Chronological age and biological maturity significantly influenced endurance (p = 0.001) and maximal strength (p = 0.020), with post-PHV players exhibiting greater gains. Chronological age and biological maturation significantly affected the physical performance of young soccer players. Relying solely on age may overlook developmental factors and underscore the need for tailored training and assessment strategies.