This study investigated changes in serum folate and B12, and associations with endurance performance and bone outcomes, in women during military training. Women (n 137) had serum folate and B12, haematological markers and endurance performance (2·4 km run) measured at the start (week 1) and end (week 13) of British Army basic training. Whole-body areal bone mineral density and markers of bone metabolism were measured at week 1. Training decreased serum folate (mean change (95 % CI), −2·3 (−3·0, −1·6) nmol ∙ l−1, P < 0·001), B12 (−16 (−32, 0) pmol ∙ l−1, P = 0·042), Hb (−0·7 (−0·9, −0·5) g ∙ dl−1, P < 0·001) and erythrocyte count (−0·2 (−0·3, −0·2) × 10^9 ∙ l−1, P < 0·001), but had no effect on mean corpuscular volume (P = 0·438) or erythrocyte distribution width (P = 0·088). There was no association between serum folate, serum B12, Hb or erythrocyte count with run time (P ≥ 0·518). Serum B12 was not associated with areal bone mineral density or bone metabolism at week 1 (P ≥ 0·152). Higher serum folate was associated with lower plasma c-telopeptide cross-links of type I collagen (standardised β (95 % CI) = −0·31 (−0·48, −0·15), P < 0·001), but not whole-body bone mineral density or plasma procollagen type I N-terminal propeptide (P ≥ 0·152). Serum folate and B12 decreased after military training in women, resulting in a high prevalence of folate deficiencies at the end of training. Low serum folate may contribute to increased bone resorption, the implications of which are unclear.