Peroxisomes are membrane-bound eukaryotic organelles that house essential metabolic pathways. Many of these pathways generate damaging reactive oxygen species (ROS) that also function as signaling molecules. In Arabidopsis thaliana, damaged or obsolete peroxisomal proteins can be degraded by the LON2 peroxisomal protease. In addition, peroxisomes can be entirely degraded through a specialized form of autophagy (pexophagy), a process that is amplified when LON2 is dysfunctional. As a first step towards identifying LON2 substrates, we used proteomic analysis to compare proteins that accumulate when LON2 is dysfunctional in the presence and absence of autophagy.