Proteins imported into mitochondria and chloroplasts are processed to remove the targeting (signal) sequence. In plants, this is known to be mediated by mitochondrial processing peptidase and stromal processing peptidase, respectively, and the peptides themselves are degraded by presequence protease (PreP). In addition to PreP, M3A family proteases have been suggested to degrade the signal peptide in many species, and this study identifies organellar oligopeptidase (OOP) as an M3A protease that carries out this function in plants. OOP was targeted to both the mitochondrial matrix and the chloroplast stroma. Moreover, it showed a substrate length restriction (8–23 amino acids; which matches many signal sequences as well as other peptide substrates) and a weak preference for hydrophobic residues but did not have a strict cleavage pattern.