Organophosphates-based pesticides were initially discovered during the first world war and have been used since then to give high quality and quantity of agricultural yield to cope with the world’s growing population. However, due to their toxicity, contaminated fields and water resources containing high levels of pesticides require decontamination to avoid any possible environmental hazards. Herein, we demonstrate the use of a highly efficient and environmentally friendly strategy to degrade such pesticides enzymatically. We recombinantly expressed and purified Methyl-parathion hydrolase (MPH) with high catalytic efficiency against paraoxon, a formerly used pesticide, herein used as an organophosphate model. The enzyme was then encapsulated within Boc-Phe-Phe peptide fibrils, resulting in an increase of its shelf life with about 50% activity after 130 days. MPH containing nanostructures were then added to a bacterial culture that consumed the paraoxon hydrolysis byproduct for growth, to obtain complete degradation of paraoxon. These results present an efficient one-pot system that can be developed as an environmentally friendly solution for pesticide decontamination.