The recent trends of nanoparticles (NPs) usage in agriculture sector is captivating. To investigate the interactions of soybean and wheat with NPs, label-free proteomic technique was used. Al2O3 and Ag-NPs under flooding stress enhanced soybean growth compared to ZnO-NPs. Among the various sizes and concentrations, 15-nm Ag-NPs promoted soybean growth. Fe NPs have stimulatory effects on wheat germination and plant growth. The physiological parameters of wheat varieties were increased on 10 ppm Cu-NPs exposure. The Ag-NPs treated soybeans have experienced less oxygen-deprivation stress through the production of less cytotoxic by-products of glycolysis. The different sizes of Ag-NPs affected the soybean growth under flooding by regulating proteins related to amino-acid synthesis and wax formation. The 30-60 nm Al2O3-NPs improved the soybean growth compared to other sizes and concentrations. Al2O3-NPs responsive proteins were related to protein synthesis/degradation, glycolysis, and lipid metabolism. Al2O3-NPs promoted the soybean growth under flooding by regulating energy metabolism and cell-death. Mitochondrion was the target organelle of Al2O3-NPs. Mitochondrial proteomics revealed the increase in abundance of voltage-dependent anion channel with 135 nm Al2O3-NPs. Al2O3-NPs of various sizes affect mitochondrial proteins under flooding by regulating membrane permeability and tricarboxylic acid cycle activity. During recovery-stage of Al2O3-NPs, S-adenosyl-L-methionine-dependent-methyltransferases and enolase were involved in mediating recovery responses. The number of proteins related to photosynthesis and protein metabolism was decreased and increased in wheat varieties treated with Fe-NPs compared to untreated plants. Fe- and Cu-NPs mend the seedling growth of wheat, which might be concomitant with the enhancement of protein abundance related to photosynthesis and glycolysis/TCA in wheat varieties. These results suggested that NPs interaction with soybean mediated the energy regulation and membrane permeability. On the other hand, NPs interaction with wheat mediated the photosynthesis and TCA.