A gas chromatography-tandem mass spectrometry (GC-MS/MS) method followed by a modified quick, easy, cheap, effective, rugged (QuEChERS) method for the analysis of three strobilurin fungicide residues (picoxystrobin, kresoxim-methyl and trifloxystrobin) in fruits, vegetables and soil was developed and validated. The three fungicides were extracted with ethyl acetate and cyclohexane (v/v = 1/1), and subsequently cleaned up using a combination of primary secondary amine and graphitized carbon black prior to GC-MS/MS analysis. The three fungicides were qualitatively determined using the multiple reaction monitoring mode with two ion transitions measured for each fungicide and evaluation by collision tests, and were determined quantitatively using the external standard method. Recovery studies were performed at three fortification levels of 0.005, 0.05, and 0.5 mg kg−1 in blank cucumber, tomato, apple, grape and soil samples. The overall average recoveries ranged from 87% to 112%, with intra-day relative standard deviations (RSDs) of 0.9% to 10.5% and inter-day RSD of 0.7% to 12.2%, respectively. The calculated limits of detection and quantification were typically below 0.006 and 0.019 μg kg−1 for GC-MS/MS. The results of the method validation confirm that this proposed method is easy and reliable for the determination of residues of strobilurin fungicides in fruits, vegetables and soil.