Longitudinal measurements of Relative Energy Deficiency in Sport (REDs) among adolescent male elite athletes are lacking. We aimed to monitor REDs indicators and their possible impact on performance in elite high-school cross-country skiing and biathlon athletes (n = 13) (16.3 ± 0.4 years, 179.4 ± 7.6 cm, 63.6 ± 8.2 kg body mass (BM), and peak oxygen uptake (VO2peak): 61.5 ± 5.3 mL/kg BM/min) every 6 months for 3 years. Protocols included assessments of energy availability (EA), body composition and bone mineral density (BMD), resting metabolic rate (RMR), disordered eating behavior, exercise addiction, VO2peak, and muscle strength. Data were analyzed using a linear mixed model. At baseline, 38% had low lumbar BMD (Z-score ≤ −1), and overall, bone health increased only slightly. VO2peak and muscle strength improved (p < 0.001), RMR decreased (p = 0.016), and no change was observed in EA or physiological or psychological REDs indicators. Conclusively, many of these young male athletes had poor bone health at baseline, and most either lost or did not achieve the expected pubertal bone mineral accrual, although no other indication of REDs was observed, while performance improved during the study period. Our findings highlight the importance of elite sports high schools focusing on screening for early detection of impaired bone health in male athletes.