The mitochondrion is the principle organelle in plant aerobic respiration, where the oxidation of organic acids to CO2 and H2O, combined with the coupling of electron transfer to O-2 via the respiratory electron transport chain to adenosine triphosphate synthesis, takes place. Plant mitochondria also have important secondary roles, such as the synthesis of nucleotides, amino acids, lipids, prosthetic groups and vitamins. They also interact with chloroplasts and peroxisomes through a series of primary metabolic pathways. By using proteomic tools such as polyacrylamide gel-based and mass spectrometry-based methods, over 400 proteins, including 30 proteins from the tricarboxylic acid cycle, 78 proteins from the electron transport chain and more than 20 proteins from amino acid metabolism pathways have been identified in mitochondria of the model plant, Arabidopsis thaliana. Beyond the mitochondrial proteome, there is growing evidence for reversible protein phosphorylation and oxidative posttranslational modifications (PTMs) that could affect functions of individual plant mitochondrial proteins or protein complexes. This review will discuss the progress in defining the PTMs that have the potential to regulate plant mitochondrial functions, with references to studies in plants, yeast and mammalian mitochondria and the development of various proteomic and affinity purification methods to study them.