Measures of body fat and lean mass may better predict important clinical outcomes in patients with cystic fibrosis (CF) than body mass index (BMI). Little is known about how diet quality and exercise may impact body composition in these patients. Dual X-ray absorptiometry (DXA) body composition, 24-h dietary recall, and physical activity were assessed in a cross-sectional analysis of 38 adolescents and adults with CF and 19 age-, race-, and gender-matched healthy volunteers. Compared with the healthy volunteers, participants with CF had a lower appendicular lean mass index (ALMI), despite no observed difference in BMI, and their diets consisted of higher glycemic index foods with a greater proportion of calories from fat and a lower proportion of calories from protein. In participants with CF, pulmonary function positively correlated with measures of lean mass, particularly ALMI, and negatively correlated with multiple measures of body fat after controlling for age, gender, and BMI. Higher physical activity levels were associated with greater ALMI and lower body fat. In conclusion, body composition measures, particularly ALMI, may better predict key clinical outcomes in individuals with CF than BMI. Future longitudinal studies analyzing the effect of dietary intake and exercise on body composition and CF-specific clinical outcomes are needed.