The enantioseparation of fenamiphos and its two main metabolites (fenamiphos sulfoxide and fenamiphos sulfone) were simultaneously achieved by CE by using a dual CD system. A mixture of 25 mM carboxymethyl-beta-CD and 10 mM hydroxypropyl-alpha-CD was added to the acetic acid/ammonia (ionic strength = 50 mM, pH 5) buffer and was suitable for the baseline resolution of all stereoisomers of analytes. A further addition of 5% methanol to the BGE increased significantly the resolution between the diastereoisomers of fenamiphos sulfoxide. An overimposed pressure (0.2 psi) was applied during the analysis in order to have better peak efficiencies and small run time. The composition of the sample solvent was found to be a crucial parameter. An amount of 15% MeOH added to the sample was a good alternative to ensure the total solubility of fenamiphos and the baseline separation of fenamiphos sulfoxide enantiomers. The extraction of pesticides from soil samples was also investigated. A methanolic extraction allowed recovering 50-75% of pesticides, which were detected by CE at the parts per million concentration level (3-100 mg/kg) with a good precision (5.1-13.2% RSD). This method was applied to soil samples and was found to be suitable to monitor the enantiomeric degradation of fenamiphos in environmental samples.