Decreases in Fe status have been reported in military women during initial training periods of 8–10 weeks. The present study aimed to characterise Fe status and associations with physical performance in female New Zealand Army recruits during a 16-week basic combat training (BCT) course. Fe status indicators – Hb, serum ferritin (sFer), soluble transferrin receptor (sTfR), transferrin saturation (TS) and erythrocyte distribution width (RDW) – were assessed at the beginning (baseline) and end of BCT in seventy-six volunteers without Fe-deficiency non-anaemia (sFer <12 µg/l; Hb ≥120 g/l) or Fe-deficiency anaemia (sFer <12 µg/l; Hb <120 g/l) at baseline or a C-reactive protein >10 mg/l at baseline or end. A timed 2·4 km run followed by maximum press-ups were performed at baseline and midpoint (week 8) to assess physical performance. Changes in Fe status were investigated using paired t tests and associations between Fe status and physical performance evaluated using Pearson correlation coefficients. sFer (56·6 (sd 33·7) v. 38·4 (sd 23·8) µg/l) and TS (38·8 (sd 13·9) v. 34·4 (sd 11·5) %) decreased (P<0·001 and P=0·014, respectively), while sTfR (1·21 (sd 0·27) v. 1·39 (sd 0·35) mg/l) and RDW (12·8 (sd 0·6) v. 13·2 (sd 0·7) %) increased (P<0·001) from baseline to end. Hb (140·6 (sd 7·5) v. 142·9 (sd 7·9) g/l) increased (P=0·009) during BCT. At end, sTfR was positively (r 0·29, P=0·012) and TS inversely associated (r –0·32, P=0·005) with midpoint run time. There were no significant correlations between Fe status and press-ups. Storage and functional Fe parameters indicated a decline in Fe status in female recruits during BCT. Correlations between tissue-Fe indicators and run times suggest impaired aerobic fitness. Optimal Fe status appears paramount for enabling success in female recruits during military training.