This study describes the ability of capillary electrochromatography (CEC) for the determination of imidacloprid and carbendazim in tomato samples. A novel liquid crystal crown ether modified hybrid silica monolithic column was synthesized, characterized and developed as separation column for the first time. Baseline separation of imidacloprid and carbendazim could be achieved using a mobile phase containing 90% (v/v) 20 mmol/L phosphate buffer (pH 7.0) and 10% (v/v) acetonitrile. The matrix matched calibration curves were linear with correlation coefficient $r^2$ > 0.9998 in the range of 0.20-10.00 mg/L. The limits of detection for imidacloprid and carbendazim were 0.061 and 0.15 mg/kg, respectively, which were below the maximum residue limits established by the European Union as well as Codex Alimentarius. Average recoveries for imidacloprid and carbendazim varied from 101.6-108.0% with relative standard deviations lower than 6.3%. This method was applied to the analysis of tomatoes collected from local markets.