We report proteomic analyses that establish the effect of cytoplasmic prion [PSI(+)] on the protein complement of yeast mitochondria. A set of 44 yeast mitochondrial proteins whose levels were affected by [PSI(+)] was identified by two methods of gel-free and label-free differential proteomics. From this set we focused on prohibitins, Phb1 and Phb2, and the mitochondrially synthesized Cox2 subunit of cytochrome oxidase. By immunoblotting we confirmed the decreased level of Cox2 and reduced mitochondrial localization of the prohibitins in [PSI(+)] cells, which both became partially restored by [PSI(+)] curing. The presence of the [PSI(+)] prion also caused premature fragmentation of mitochondria, a phenomenon linked to prohibitin depletion in mammalian cells. By fractionation of cellular extracts we demonstrated a [PSI(+)]-dependent increase of the proportion of prohibitins in the high molecular weight fraction of aggregated proteins. We propose that the presence of the yeast prion causes newly synthesized prohibitins to aggregate in the cytosol, and therefore reduces their levels in mitochondria, which in turn reduces the stability of Cox2 and possibly of other proteins, not investigated here in detail.