The presence of toxic metals in vegetables of daily consumption is a concern for human health. Little is known about the concentration of toxic metals in vegetables sold in markets in Quito, Ecuador, and the corresponding risk to the population. This study aimed to measure the concentration of cadmium (Cd), and lead (Pb) in tomatoes, carrots, and lettuce, to estimate the risk for human health, and to determine the trophic transfer factor using Drosophila melanogaster flies. Vegetable samples were obtained from four local markets in Quito to measure the concentration of Cd and Pb (expressed in mg/kg of dry weight) in the vegetables by microwave-assisted acid digestion and atomic absorption spectrophotometry. Drosophila melanogaster flies were fed with contaminated vegetables to determine de trophic transfer factor of metals in the trophic chain. Our results showed the highest accumulation of Pb and Cd occurred in lettuce. In all cases, the Pb and Cd concentrations exceeded the maximum levels established by the Food and Agriculture Organization. However, the daily intake of metals and the health risk index showed no risk from daily consumption. Pb’s trophic transfer factor was excessively high in the tomato-fed flies, showing transference and accumulation in the flies. Cadmium concentration in tomato-fed flies was also the highest among the three vegetables. The trophic chain transfer of toxic metals from vegetables to Drosophila has been observed through a high accumulation of these metals in flies, and this suggests a negative impact on both human health and ecosystems.