The chemical fungicide fludioxonil is widely used to control post-harvest fungal disease in cherries. This study was implemented to investigate the dissipation behaviours and residues of fludioxonil on cherries. A reliable and efficient analytical method was established. Cherry samples from four product areas were analyzed by QuEChERS and HPLC-MS/MS methods with acceptable linearity (R2 > 0.99), accuracy (recoveries of 81–94%), and precision (relative standard deviation of 2.5–11.9%). The limits of quantification (LOQs) and limits of detection (LODs) of cherries were 0.01 mg/kg and 0.005 mg/kg. The dissipation of fludioxonil on cherries followed first order kinetics with half-lives of 33.7–44.7 days. The terminal residues of fludioxonil were all lower than 5.00 mg/kg, which is the MRL recommended by the European Commission. According to Chinese dietary patterns and terminal residue distributions, the risk quotient (RQs) of fludioxonil was 0.61%, revealing that the evaluated cherries exhibited an acceptably low dietary risk to consumers.
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