The growing technology and development in the agriculture industry has led to the introduction of genetically modified organisms (GMO’s) crops having which have high resistance to insecticides, thus there is a tremendous rise in the use of the pesticides/insecticide worldwide. The underlying concern is about the possible health issue related to their residues in the daily dietary intake viz sources such as water, fruits, vegetables and grains. Therefore, various regulatory bodies have set the maximum residue limits for safe use of these pesticides or insecticides in agriculture land. Secondly, regardless of the rising debate or controversies about the GMO’s among society and producer, their cultivation is constantly increasing. As the impact of cultivating these crops on human health are under study, more than 50 countries have mandated the labelling of these GMO’s proteins to ensure the right to information to the consumers. Although these pesticides/insecticides and GMO’s can be detected precisely using gold standard analytical methods in the food matrix, but these methods require an expert to handle, and stringent sample pre-processing steps. Thus, there is a high demand for the portable, on-field device which can be used at the consumer levels requiring no pre-sample processing steps. In our work, we explore the use of the electrochemical assay method to detect the pesticides such as Chlorpyrifos, Glyphosate and GMO proteins in high fat and low-fat food matrices. The assay-based electrochemical multiplex sensor has been developed by modifying the screen-printed Au-electrode/carbon electrode substrate with the respective antibody at optimized concentrations. The real low-fat and high-fat sample matrices has been prepared by simply blending the mix using home blender. The real sample matrix spiked with the pesticides /GMO protein were tested for calibrated dose response from 0.3 ng/mL- 243 ng/mL, and the limit of detection of less than < 10 ng/mL were observed using this developed electrochemical portable device method. Such portable electrochemical device approach could be a promising on-field sensing tool for the pesticide and GMO protein detection.