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), haemoglobin (−0.7 [−0.9, −0.5] g∙dL-1, p < 0.001), and red blood cell (RBC) 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, haemoglobin, or RBC 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.