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• Lactobacillus plantarum can degrade 81.28% of dimethoate in milk rapidly. • Enzyme is the main mechanism for Lactobacillus plantarum to degrade dimethoate. • Five degradation products of dimethoate were identified by UPLC-QTOF/MS. Bioremediation of pesticides in contaminated foodstuffs using probiotics has attracted great attention in recent years, but some intermediate products may have profound effects on the toxicity of treated food. Therefore, this work studied the degradation mechanism of dimethoate in milk by L. plantarum, and analyzed the toxicity of degradation products. The results showed that under the optimal conditions, L. plantarum can degrade 81.28% of dimethoate. Dimethoate had high binding affinities to phosphatase with the free energy of –16.67 kcal/mol, and amino acid residues, Gln375 and SER415 played important roles in the catalysis process. Five degradation products were identified using UPLC-QTOF/MS, and their toxicity was estimated using quantitative structure–activity relationship models. Some intermediate products were predicted to be toxic, which should not be ignored, but the overall toxicity of milk decreased after fermentation. Furthermore, the pH and titratable acidity of the fermented milk were 4.25 and 85 ◦T, respectively. [ABSTRACT FROM AUTHOR]