Psychomotor development plays an important role in neuromuscular regulation, movement efficiency, and football-specific performance during early adolescence. This study investigated changes associated with an integrated psychomotor-oriented intervention program in psychomotor abilities, technical performance, and functional physiological responses in U13 football players. A longitudinal quasi-experimental pretest–posttest design was applied to 17 male youth football players during the competition season. The 12-week intervention program was integrated into regular football training and included psychomotor, neuromuscular, coordinative, and football-specific exercises. Psychomotor assessment included sprint performance, postural stability and control, agility, and reactive neuromuscular parameters, complemented by football-specific technical tests and functional match monitoring using the Polar Vantage V system. An external comparative U13 team (n = 17) was additionally evaluated for football-specific technical performance. Significant within-group improvements were observed in 20-m sprint performance (Δ = −0.19 s; p < 0.001; d = −1.13), lateral bipedal postural stability (Δ = +20%; p < 0.001; d = 1.35), and vertical bipedal postural control (Δ = +10%; p = 0.006; d = 0.77). All three technical tests improved significantly within the intervention group (Test 1: p = 0.002, d = 0.88; Test 2: p = 0.016, d = 0.75; Test 3: p = 0.037, d = 0.63), while between-group comparisons of change scores were not statistically significant. Functional monitoring during official match play identified a significant reduction in Speed Z3 exposure (p = 0.016; d = −0.70), while no statistically significant changes were observed in the other physiological or locomotor variables. Spearman correlation analyses identified significant associations among psychomotor, technical, and functional variables (ρ = −0.753 to −0.488; p < 0.05). Given the small sample, non-randomized design, incomplete multidimensional assessment in the comparative group, and absence of biological maturation assessment, the findings should be interpreted as preliminary evidence of within-group changes associated with psychomotor-oriented training rather than as definitive causal effects.