A carbon paste electrode modified with ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate) and MoO3/WO3 nanocomposite (MoO3/WO3/ILCPE) as an electrochemical sensor was developed for co-detection of tartrazine and carmoisine. Differential pulse voltammetry (DPV) method was applied to evaluate the electrochemical responses of tartrazine and carmoisine, the results of which confirmed a significant improvement of electrochemical behaviors on the modified electrode surface. High peak separation of oxidation (800 mV) made possible the co-detection of tartrazine and carmoisine. The DPV data in 0.1 M phosphate buffer solution at a pH value of 7.0 made it possible to develop a method for determining carmoisine in the dynamic range of 0.5–100 µM with the limit of detection of 0.15 µM. Also, the fabricated sensor showed good stability and selectivity. Our modified sensor could successfully detect these compounds in the real fruit specimens.