Rhomboid proteases are present in bacteria, insects, yeasts, parasites, mammals and plants. These proteases are part of the regulated intramembrane proteolysis mechanism for controlling processes such as development, stress response, lipid metabolism and mitochondrial membrane remodeling. Specific rhomboid protease substrates linked to these processes have been identified from insects to mammals, but not for plants. Identification of a link is a key step for elucidating the role of each rhomboid protease. Here, using a yeast mitochondria-based approach, we report evidence of a potential link between a plastid translocon component and organellar rhomboid proteases. This identification expands the types of processes involving regulated intramembrane proteolysis potentially to include at least one aspect of plastid protein transport.