PURPOSE: This study aimed to investigate the effect of supplementary energy on bone formation and resorption during arduous military training in energy deficit. METHODS: Thirty male soldiers completed an 8-wk military combat course (mean ± SD, age = 25 ± 3 yr, height = 1.78 ± 0.05 m, body mass = 80.9 ± 7.7 kg). Participants received either the habitual diet (control group, n = 15) or an additional 5.1 MJ·d-1 to eliminate the energy deficit (supplemented group, n = 15). Circulating markers of bone formation and resorption, and reproductive, thyroid, and metabolic status, were measured at baseline and weeks 6 and 8 of training. RESULTS: Bone-specific alkaline phosphatase decreased in controls (-4.4 ± 1.9 μg·L-1) and increased in the supplemented group (16.0 ± 6.6 μg·L-1), between baseline and week 8 (P < 0.001). Procollagen type 1 N-terminal propeptide increased between baseline and week 6 for both groups (5.6 ± 8.1 μg·L-1, P = 0.005). Beta carboxy-terminal cross-linking telopeptide of type 1 collagen decreased between baseline and week 8 for both groups (-0.16 ± 0.20 μg·L-1, P < 0.001). Prolactin increased from baseline to week 8 for the supplemented group (148 ± 151 IU·L-1, P = 0.041). The increase in adiponectin from baseline to week 8 was higher in controls (4.3 ± 1.8 mg·L-1, P < 0.001) than that in the supplemented group (1.4 ± 1.0 mg·L-1, P < 0.001). Insulin-like growth factor binding protein-3 was lower at week 8 than baseline for controls (-461 ± 395 ng·mL-1, P < 0.001). CONCLUSION: The increase in bone-specific alkaline phosphatase, a marker of bone formation, with supplementation supports a role of energy in osteoblastic activity; the implications for skeletal adaptation and stress fracture risk are unclear. The mechanism is likely through protecting markers of metabolic, but not reproductive or thyroid, function.