Exercising women with menstrual disturbances frequently display a low resting metabolic rate (RMR) when RMR is expressed relative to body size or lean mass. However, normalizing RMR for body size or lean mass does not account for potential differences in the size of tissue compartments with varying metabolic activities. To explore whether the apparent RMR suppression in women with exercise-associated amenorrhea is a consequence of a lower proportion of highly metabolically active tissue compartments or the result of metabolic adaptations related to energy conservation at the tissue level, RMR and metabolic tissue compartments were compared among exercising women with amenorrhea (AMEN, n=42) and exercising women with eumenorrheic, ovulatory menstrual cycles (OV, n=37). RMR was measured using indirect calorimetry and predicted from the size of metabolic tissue compartments as measured by dual-energy X-ray absorptiometry (DXA). Measured RMR was lower than DXA-predicted RMR in AMEN (1215±31 vs. 1327±18 kcal/d, p<0.001) but not in OV (1284±24 vs. 1252±17, p=0.16), resulting in a lower ratio of measured to DXA-predicted RMR in AMEN (91±2%) vs. OV (103±2%, p<0.001). AMEN displayed proportionally more residual mass (p<0.001) and less adipose tissue (p=0.003) when compared to OV. A lower ratio of measured to DXA-predicted RMR was associated with lower serum total triiodothyronine (=0.38, p<0.001) and leptin (=0.32, p=0.004). Our findings suggest that RMR suppression in this population is not the result of a reduced size of highly metabolically active tissue compartments but due to metabolic and endocrine adaptations at the tissue level that are indicative of energy conservation.