Updated project metadata. Hundreds of mitochondrial precursor proteins are synthesized in the cytosol and imported into mitochondria in a post-translational reaction. The early stages in mitochondrial protein targeting are poorly understood. Here we show that in baker’s yeast, the cytosol has the capacity to transiently store matrix-destined precursors in dedicated deposits which we named MitoStores. MitoStores are strongly induced when the import into mitochondria is competitively inhibited by clogging the mitochondrial import sites, but also found under physiological conditions when cells grow on non-fermentable carbon sources. MitoStores contain a specific subset of nuclear encoded mitochondrial proteins, in particular those with N-terminal mitochondrial targeting sequences. The cytosolic heat shock proteins Hsp42 and Hsp104 control MitoStore formation, thereby suppressing the toxic potential of accumulating mitochondrial precursor proteins. Thus, the cytosolic protein quality system plays an active role during early stages in mitochondrial protein targeting by the coordinated localized sequestration of mitochondrial precursor proteins.