Background: A decline in resting energy expenditure (REE) beyond that predicted from changes in body composition has been noted following dietary-induced weight loss. However, it is unknown whether a compensatory down-regulation in REE also accompanies exercise-induced weight loss, or whether this adaptive metabolic response influences energy intake (EI). Methods: Thirty overweight and obese women (BMI = 30.6 ± 3.6kg.m-2) completed 12 weeks of supervised aerobic exercise (EX). Body composition, metabolism, EI and metabolic-related hormones were measured at baseline, week six and post-intervention. The metabolic adaptation i.e. difference between predicted and measured REE was also calculated post-intervention (MApost), with REE predicted using a regression equation generated in an independent sample of 66 overweight and obese women (BMI = 31.0 ± 3.9kg.m-2). Results: While mean predicted and measured REE did not differ post-intervention, 43% of participants experienced a greater than expected decline in REE (-102.9 ± 77.5kcal.day-1). MApost was associated with the change in leptin (r = 0.47; p = 0.04), and the change in resting fat (r = 0.52; p = 0.01) and carbohydrate oxidation (r = -0.44; p = 0.02). Furthermore, MApost was also associated with the change in EI following EX (r = -0.44; p = 0.01). Conclusions: Marked variability existed in the adaptive metabolic response to EX. Importantly, those who experienced a down-regulation in REE also experienced an up-regulation in EI, indicating that the adaptive metabolic response to exercise influences both physiological and behavioural components of energy balance in a co-ordinated fashion.