This study assessed energy and fat metabolism in a well phenotyped cohort of patients with organic acidemias using non-invasive MR spectroscopy. 31P and 1H spectra of the liver as well as 1H spectra of the muscle were acquired in 27 patients and 30 healthy controls (age-, sex-, BMI-matched). We found higher liver fat content in patients with propionic acidemia. The level of creatine in the soleus muscle was higher in patients with methylmalonic acidemia and propionic acidemia. In conclusion, the results provide evidence for previously unknown abnormalities of liver fat and muscle energy metabolism in patients with organic acidemias.