Bisphenol A (BPA), a widely distributed organic compound, is toxic to animals and plants. Here we show the mechanism of BPA detoxification by melatonin (MEL) in tomato, which is otherwise poorly understood in plants. BPA treatment decreased the quantum yield of photosystem II (Fv/Fm) and increased the membrane lipid peroxidation and reactive oxygen species (ROS) accumulation dose-dependently, whereas exogenous MEL alleviated the BPA effects on Fv/Fm, lipid peroxidation, ROS accumulation and BPA uptake. Furthermore, BPA elevated the glutathione (GSH) content, activities of glutathione S-transferase (GST), and glutathione reductase (GR), and the transcript levels of GSH1, GR1, GST1 and MEL biosynthesis genes (COMT, T5H, and SNAT), whereas BPA + MEL showed even a more profound induction. Silencing GSH1, GR1 and GST1 genes compromised the BPA detoxification potential of tomato plants as revealed by an increased level of ROS, lipid peroxidation and BPA uptake, and a decreased Fv/Fm and GST activity; these changes were alleviated by MEL application. Under in vitro conditions, BPA was glutathionylated by GSH, which was further catalyzed by GST to cysteine and N-acetylcysteine conjugates. These findings suggest a crucial role for MEL in BPA detoxification via GSH and GST, and can be useful to reduce BPA residue for food safety.