chaperone and protease functions of lon protease 2 modulate the peroxisomal transition and degradation with autophagy balancing repair and degradation is essential for maintaining organellar and cellular homeostasis peroxisomes are ubiquitous organelles in eukaryotic cells that play pivotal roles in cell survival however the quality control mechanism used to maintain peroxisomes is unclear here we demonstrate that lon protease 2 lon2 which is encoded by aberrant peroxisome morphology 10 apem10 is responsible for the functional transition of peroxisomes with autophagy the arabidopsis apem10 mutant displayed accelerated peroxisome degradation and a dramatically reduced number of peroxisomes lon2 deficiency caused enhanced peroxisome degradation by autophagy and peroxisomal proteins accumulated in the cytosol due to a decrease in the number of peroxisomes we also show the proteolytic consequence of lon2 for the degradation of peroxisomal proteins and we demonstrated that unnecessary proteins are eliminated by lon2 and autophagydependent degradation pathways during the functional transition of peroxisomes lon2 plays dual roles as an atpdependent protease and a chaperone we show that the chaperone domain of lon2 is essential for the suppression of autophagy whereas its peptidase domain interferes with this chaperone function indicating that intramolecular modulation between the proteolysis and chaperone functions of lon2 regulates degradation of peroxisomes by autophagy