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-week military combat course (mean ± SD, age 25 ± 3 years, 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 week 6 and 8 of training. Results: Bone ALP 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). P1NP increased between baseline and week 6 for both groups (5.6 ± 8.1 μg•L -1 , P = 0.005). βCTX 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 the supplemented group (1.4 ± 1.0 mg•L -1 , P < 0.001). IGF 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 ALP, a marker of bone formation, with supplementation supports a role of energy in osteoblastic activity; the implications for skeletal adaptation and stress fracture risk is unclear. The mechanism is likely through protecting markers of metabolic, but not reproductive or thyroid, function.