Insect pests cause one-third of grain loss during storage. This should be minimized through sustainable management to assure food security. This study describes development of nano-formulated biopesticides for managing stored product insect pests Callosobruchus maculatus (Fabricius) (Chrysomelidae; Coleoptera) and Trogoderma granarium (Everts) (Dermestidae; Coleoptera). Cysteine protease (PeuCP) from Populus euphratica was extracted, purified (by ammonium sulfate saturation prior to gel filtration chromatography), and identified through LC-MS/MS. The molecular interaction of PeuCP with substrate (chitin) was documented via in-silico study. The PeuCP was formulated with Graphene Quantum Dots (GQDs) and Zinc Oxide Nanoparticles (ZnO NPs). The insecticidal activity of PeuCP was assessed by bioassays against two stored product insect pests at three concentrations (10, 5 and 2.5 mg/g). Computational analysis showed molecular interaction of PeuCP at five potential sites for ligand (N-acetyl-D-glucosamine) binding in which the strongest site with the highest drug score (Site-1) was located near N-terminus. The insecticidal assays of PeuCP without nano-formulation revealed inhibited population buildup of C. maculatus and delayed life stages development in T. granarium. The growth inhibition of tested insects confirmed the substrate binding of PeuCP. The results also revealed increased insecticidal activity of PeuCP after nanoformulations, among which GQDs nanoformulation was more promising. Nanoformulated PeuCP had the potential to control stored grain insect pests as alternative to chemical insecticides.