Recently, the spreading of agricultural pesticides in the food chain, waterbodies, and soil has become a major concern, creating enormous challenges for regulatory bodies. Agricultural pesticide utilization has increased for improved crop production to fulfill the demands of a huge population, resulting in pesticide pollution throughout the world. Developing a highly efficient in-situ system for the sensing and quantifying of pesticides is the need of the hour to control pesticide pollution in India and globally. Utilization of intensive chemicals in conventional nanomaterial synthesis could produce toxic by-products. Bio-based methods could be highly efficient and eco-friendly alternatives for nanoparticle synthesis. Herein, we report the formation of silver nanoparticles (AgNPs) using a vegetal extract of Citrus Limon by a microwave-assisted method for electrochemical sensing of carbendazim. The average particle size of highly crystalline and mesoporous bio-based AgNPs was 10.33 ± 2.3 nm with a BET surface area of 392.5 m2/g. AgNPs/GCE decreases the charge transfer resistance from 2830 to 474 KΩ and increases the electroactive surface area by 2.83 times that of bare GCE. The detection limit, quantification limit, sensitivity, and linear concentration range of the AgNPs/GCE were 0.279 µM, 0.931 µM, 0.668 µA. µM−1.cm−2, and 0–50 µM, respectively. The proposed sensor showed a 3.53% decline in the peak current up to the 5th cycle of carbendazim sensing. Moreover, AgNPs/GCE exhibited excellent sensing performance with high stability for electrocatalytic sensing of carbendazim.