FES1a is an auxiliary molecular chaperone of heat shock protein 70 (HSP70), and the fes1a mutant is defective in acquired thermotolerance. As an efficient clearance pathway, autophagy is a positive regulator of basal thermotolerance and a negative regulator of heat stress memory, but its function in acquired thermotolerance is unclear. Proteomic analysis revealed that blocking constitutive autophagy leads to the accumulation of peroxisomes and related metabolic pathways within the peroxisomes.