Melatonin has an important anti-aging role in plant physiology. We tested the effects of long-term melatonin exposure on metabolic status and protein degradation during natural leaf senescence in trees of Malus hupehensis Rehd. The 2-month regular supplement of 100 μm melatonin to the soil once every 6 days altered the metabolic status and delayed protein degradation. For example, leaves from treated plants had significantly higher photosynthetic activity, chlorophyll concentrations, and levels of three photosynthetic end products (sorbitol, sucrose, and starch) when compared with the control. The significant inhibition of hexose (fructose and glucose) accumulation possibly regulated the signaling of MdHXK1, a gene for which expression was also repressed by melatonin during senescence. The plants also exhibited better preservation of their nitrogen, total soluble protein, and Rubisco protein concentrations than the control. The slower process of protein degradation might be a result of melatonin-linked inhibition on the expression of apple autophagy-related genes (ATGs). Our results are the first to provide evidence for this delay in senescence based on the metabolic alteration and protein degradation.