Nitrogen-limiting condition is essential for citric acid production by Yarrowia lipolytica . Mitochondrial protein expression profiles of Y. lipolytica IMUFRJ 50,682 cells cultivated in biomass proliferation medium (YPG medium, yeast extract, peptone and glycerol) and citric acid production medium (CA medium) were analyzed to identify differences in expressed proteins in response to medium composition. The identification of 45 proteins in mitochondria of YPG medium cells and 48 proteins in mitochondria of CA medium cells were possible with proteomic analyses. Only 11 proteins were common to both conditions, showing a different expression pattern in relation to limiting and non-limiting nitrogen conditions. For both conditions, most proteins (52%—CA medium, 46%—YPG medium) were related to energy metabolism. CA medium cells expressed more carbohydrate metabolism proteins (six proteins) then YPG medium cells (three proteins) and the opposite was detected for translation proteins.