Plant mitochondria link the cellular processes of carbon and nitrogen metabolism through the tricarboxylic acid cycle and the photorespiratory cycle. Environmental stresses lead to damage of specific mitochondrial targets through the direct action of reactive oxygen species and indirect action of lipid peroxidation products. Uncovering the extent of this damage, the exact sites of damage and the mechanisms of avoidance and/or repair remains a largely unresearched challenge for plant scientists. Damage to Fe-S centres and proteins containing lipoic acid moieties appear to predominate in current reports. Substantial evidence that both TCA cycle and photorespiratory capacity of mitochondria are sensitive sites for damage is highlighted and the implications for mitochondrial-dependent carbon and nitrogen metabolism are discussed.