In this study, the original Quick, Easy, Cheap, Effective, Rugged and Safe method was used for the extraction of imidacloprid and pyrimethanil followed by a rapid clean‐up through dispersive solid‐phase extraction technique with primary secondary amine sorbent and magnesium sulfate in shallot. Residues were analyzed using LC‐tandem mass spectrometry in positive‐ion electrospray ionization mode. The limits of detection and quantification were estimated to be 0.006 and 0.02 mg/kg, respectively. The samples were fortified at two different concentration levels (0.2 and 1.0 mg/kg), and the recoveries ranged between 79.7 and 83.9% with relative standard deviation values < 6%. The method was successfully applied for the establishment of the pre‐harvest residue limits (PHRL). The rate of disappearance of imidacloprid and pyrimethanil on shallot was described with first‐order kinetics (imidacloprid, y2 = 0.9670; pyrimethanil, y2 = 0.9841), with half‐lives of 2.87 and 2.08 days, respectively. Based on the dissipation patterns of the pesticide residues, the PHRL was recommended at 7.86 mg/kg for 14 days (PHRL14) and 1.98 mg/kg for 7 days (PHRL7) before harvest for imidacloprid, and 21.64 mg/kg for 7 days (PHRL7) and 9.28 mg/kg for 4 days (PHRL4) before harvest for pyrimethanil in shallot. Copyright © 2012 John Wiley & Sons, Ltd.