During leaf senescence, autophagy is essential for nutrient recycling and remobilization, and for plant productivity. Metabolome and transcriptome studies performed on autophagy mutants revealed major disorders in nitrogen, carbon, and redox metabolisms. Analysis showed that autophagy mutants are depleted of antioxidant anthocyanin molecules. Transcriptome analysis revealed that the depletion of anthocyanin is due to the downregulation of the master genes encoding the enzymes and regulatory proteins involved in the flavonoid pathway. The hyperaccumulation of salicylic acid and the depletion of anthocyanin in autophagy mutants might result from the rerouting of carbon resources in the phenylpropanoid pathway and amplify oxidative stress in autophagy mutants.