Massive weight loss achieved through dietary restriction or bariatric surgery improves health and disease outcomes. However, such profound weight loss usually results in an undesirable loss of fat-free mass (FFM), the primary determinant of resting metabolic rate (RMR). Loss of FFM together with suppression of RMR may predispose to weight regain. Accordingly, an important goal during weight loss is to maximize the loss of body fat and minimize the loss of metabolically active FFM. Several investigators have suggested that adding exercise to a weight-loss program may preserve FFM and attenuate the suppression of RMR during weight loss. This observational study was designed to determine whether participation in an intensive program consisting of diet restriction and vigorous exercise would help preserve FFM and maintain RMR. Body composition was measured with dual-energy x-ray absorptiometry. Resting metabolic rate was measured by indirect calorimetry, and total daily energy expenditure was determined using doubly labeled water. Testing was conducted at baseline (n = 16), 6 weeks (n = 11), and 30 weeks (n = 16). Participants were severely obese at baseline with a body mass index of 49.4 ± 9.4 kg/m2, and a body weight of 149.2 ± 38.0 kg, with 49% ± 5% body fat. By week 30, participants lost nearly 40% of their initial body weight (38% ± 9%), 17% from FFM and 83% from fat. There was a decline in RMR out of proportion to the decrease in body mass; differences between the actual and predicted RMR values (metabolic adaptation) were substantial (−244 ± 231 kcal/d at week 6 and −504 ± 171 kcal/d at week 30; both P < 0.05) compared with baseline values. Physical activity expenditure increased by 10.2 ± 5.1 kcal/kg·per day at week 6 and 6.0 ± 4.1 kcal/kg·per day at week 30 (both P < 0.05 compared with baseline and each other). These findings show that despite relative preservation of FFM, marked slowing of resting metabolism out of proportion to weight loss is not avoided by the addition of an exercise program. Persistence of metabolic adaptation during weight maintenance may predispose to weight regain unless high levels of physical activity or significant caloric restriction are maintained.