This study aimed to quantify the relationships among internal training load, wellness, physiological, isokinetic profile, and technical performance and assessed changes before and after a six-week pre-season structured combining physical fitness, small-sided-game and skill-based training program in young soccer players. Forty-five national-level young male soccer players (16.8 ± 0.9 years) were evaluated. There were no significant correlations between the wellness index and the physiological, isokinetic, or specific soccer skill parameters. Moderate correlations were observed between fatigue and stress (r = 0.47, moderate, p < 0.01), fatigue and average muscle soreness (r = 0.38, moderate, p = 0.01), and a large correlation between average stress and muscle soreness (r = 0.53, large, p < 0.01) were presented. All physiological, isokinetic, and technical parameters improved after a six-week pre-season training program (0.1 to −61.0%). Significant alterations in the physiological domain were observed after a six-week period, particularly in the fatigue index of the Bangsbo sprint test, YO-YO IR1 performance, and YO-YO peak La- (p < 0.01; −61.0%, 25.3%, and −19.8%, respectively). As such, the implementation of structured training and the monitoring of stress responses can lead to appropriate adaptation and balancing in the psychological and physical well-being of young national-level soccer players, particularly in the pre-season period.