Different cell types, organs and tissues shape their mitochondrial proteome according to the cellular environment that is dictated by differentiation, development and metabolic status. Under each circumstance, members of multigenic families that encode mitochondrial proteins are differentially expressed to meet the mitochondrial metabolic demand. However, the mitochondrial proteome may drastically change in response to stress conditions. Examples of the changes in mitochondrial protein expression caused by stress are represented by the energy-dissipating mitochondrial uncoupling protein (UCP) and alternative oxidase (AOx). UCP and AOx belong to multigenic families in plants, and their members, which are expressed in a time/tissue specific manner, respond differentially to stress conditions. In general, UCP and AOx are not expressed at the same levels concurrently in the same tissue, and the level of each protein varies in each stress condition. In addition, under non-stress conditions, UCP is expressed at much higher levels compared with AOx. The role of their differential expression in plant growth, development and response to stress is discussed.