Besides characteristic neurologic and musculoskeletal symptoms, children with mitochondrial dysfunction often present with feeding problems and failure to thrive. Substrate depletion for the respiratory chain has an effect on energy expenditure. Secondary mitochondrial dysfunction has been reported in severe chronic malnutrition. We evaluated the nutritional state, the growth parameters, and the metabolic condition in 172 children undergoing muscle biopsy for a suspected disorder of the oxidative phosphorylation system (OXPHOS). We performed dietary evaluation and initiated nutritional intervention when needed before the biopsy. Mitochondrial dysfunction was confirmed by detection of enzyme-complex deficiencies and/or by mutations in 83 children, in 14 patients no biochemical abnormalities were found. In the whole study group, and in the subgroup with enzyme-complex deficiency and/or mutation, a significant correlation was found between the mitochondrial production of adenosine triphosphate (ATP) and the age-related body mass index (BMI). Nutritional state and growth should be considered by interpreting the results of ATP-production in fresh muscle biopsy. Because of a positive correlation between the age-appropriate BMI and the ATP-production, we strongly advise optimizing the nutritional state preceding the muscle biopsy in children with a suspected OXPHOS-disorder. Dietary intervention remains although challenging because of frequent gastrointestinal problems and eating disorders.