Growing organic food is becoming a challenging task with increasing demand. Food fraud activity has increased considerably with the increase in population growth. Consumers cannot visually distinguish between conventional and organically grown food products. Spectroscopic methodologies are presented to identify chemicals in food, thereby identifying organic and conventional food. Such spectroscopic techniques are laboratory-based, take more time to produce an outcome, and are costlier. Thus, this research designed a portable, low-cost multispectral sensor system to discriminate between organic and conventional vegetables. The designed multispectral sensor system uses a wavelength range (410 nm–940 nm) that includes three bands, namely visible (VIS), ultraviolet (UV) and near-infrared (NIR) spectra, to enhance the accuracy of detection. Tomato, brinjal and green chili samples are employed for the experiment. The organic and conventional discrimination problem is formulated as a classification problem and solved through random forest (RF) and neural network (NN) models, which achieve 92% and 89% accuracy, respectively. A two-stage enhancement mechanism is proposed to improve accuracy. In the first stage, the fuzzy logic mechanism generates additional feature sets. Ant colony optimization (ACO) algorithm-based parameter tuning and feature selection are employed in the second stage to enhance accuracy further. This two-stage improvement mechanism results in 100% accuracy in discriminating between organic and conventional vegetable samples. The detected adulterant is displayed on a web page through an IoT-developed application module to be accessed from anywhere.