Introduction <p>Monitoring training for optimal performance outcomes requires input information for decision-making. Identifying quantitative variables that can predict exercise-induced adaptations asynchronously is methodologically challenging and likely requires a large matrix of data.</p> Objectives <p>This study aimed to track early metabolite changes as potential predictors of improvements in performance-related variables following a 5-week military training program.</p> Methods <p>We performed metabolomic analysis using ¹H-nuclear magnetic resonance to quantify 82 urinary metabolites in young cadets before and during the first week of a five-week military training program. Performance-related variables were measured pre- and post-training. Statistical analyses were performed using parametric or non-parametric tests, depending on data distribution, with adjustments for multiple comparisons. Relationships between early changes in metabolites (on days 2 and 7) and performance outcomes were assessed using correlation analysis. Multiple regression models were developed, excluding highly correlated variables, to predict performance outcomes at the end of the training.</p> Results <p>Fifteen metabolites whose early changes (on days 2 and 7) significantly predicted gains in performance variables (body mass index, R² = 0.48; body mass, R² = 0.60; jump power, R² = 0.60; jump height, R² = 0.69; VO_2max, R² = 0.83) assessed four weeks later were identified. Except for an increase in trigonelline, the other 14 metabolites showed significant decreases (50–90%) from pre-training values. Among these, citrate, 4-pyridoxate, and ascorbate were most important for the predictive models.</p> Conclusions <p>Urinary metabolomics can suggest changes in metabolites that predict later performance gains. The identified metabolites are associated with vitamins, coenzymes, or energy metabolism intermediates.</p>