Abstract <p> Energy deficiency among exercising females is associated with metabolic adaptations to conserve energy, menstrual cycle disturbances, and poor bone health. The purpose of this paper is to describe how a randomized controlled trial (clinicaltrials.gov: NCT00392873) with a nutritional intervention influenced indicators of metabolic status and whether these indicators are associated with menstrual recovery among oligo/amenorrheic (Oligo/Amen) exercising women. Recreational and competitive female athletes with Oligo/Amen were randomized to a control group (Oligo/Amen Control, <i>n</i> = 36; 20.7 ± 0.5 yrs; 59.1 ± 1.3&#xa0;kg; 21.3 ± 0.4&#xa0;kg/m²) or an intervention group (Oligo/Amen + Cal, <i>n</i> = 40; 21.3 ± 0.5 yrs; 55.0 ± 1.0&#xa0;kg; 20.4 ± 0.3&#xa0;kg/m²), who increased energy intake 20–40% above baseline energy needs for 12 months. Daily energy intake and expenditure, resting metabolic rate (RMR), body composition, and metabolic hormones, including total triiodothyronine (TT3), leptin, ghrelin, insulin-like growth factor-1 (IGF-1), and peptide YY, were assessed every 3 months. Reproductive function was monitored continually. Oligo/Amen + Cal females significantly increased energy intake (<i>p</i> = 0.002) and energy availability (<i>p</i> = 0.003) with a balanced increase in macronutrients. Percent body fat, TT3, and IGF-1 also significantly increased from baseline in the Oligo/Amen + Cal group compared with the Control group (<i>p</i> &lt; 0.05) whereas leptin and RMR did not change. Longitudinal measures of body mass, body fat, and IGF-1 were significant predictors of menstrual recovery (<i>p</i> &lt; 0.02). A nutritional intervention of increased energy intake in Oligo/Amen exercising females improved metabolic hormones but didn’t completely reverse signs of metabolic compensation. Changes in body mass, body fat, and IGF-1 in response to a nutritional intervention may represent important factors for monitoring progress toward menstrual recovery.</p>