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In the present study, we attempted to use melatonin combined with germination treatment to remove pesticide residues from contaminated grains. High levels of pesticide residues were detected in soybean seeds after soaking with chlorothalonil (10 mM) and malathion (1 mM) for 2 hours. Treatment with 50 μM melatonin for 5 days completely removed the pesticide residues, while in the control group, only 61–71% of pesticide residues were removed from soybean sprouts. Compared with the control, melatonin treatment for 7 days further increased the content of ascorbic acid (by 48–66%), total phenolics (by 52–68%), isoflavones (by 22–34%), the total antioxidant capacity (by 37–40%), and the accumulated levels of unsaturated fatty acids (C18:1, C18:2, and C18:3) (by 17–30%) in soybean sprouts. Moreover, melatonin treatment further increased the accumulation of ten components of phenols and isoflavones in soybean sprouts relative to those in the control. The ability of melatonin to accelerate the degradation of pesticide residues and promote the accumulation of antioxidant metabolites might be related to its ability to trigger the glutathione detoxification system in soybean sprouts. Melatonin promoted glutathione synthesis (by 49–139%) and elevated the activities of glutathione-S-transferase (by 24–78%) and glutathione reductase (by 38–61%). In summary, we report a new method in which combined treatment by melatonin and germination rapidly degrades pesticide residues in contaminated grains and improves the nutritional quality of food. [ABSTRACT FROM AUTHOR]