Nanoparticles are playing an influential role in various fields of life. Among them, Aluminum oxide (Al2O3) nanoparticles have been extensively produced and used in various commercial and agricultural products. Soybean, which is a flooding intolerant legume, exhibits severe reduction in growth resulting in economical loss. To elucidate Al2O3 nanoparticles role in recovery of soybean under flooding stress, a gel free proteomic technique was used. Flooding exposure for 2 and 4 days reduced seedling weight; however, soybean unveiled recovery at 50 ppm after stress removal. Fresh weight of root including hypocotyl was improved at 50 and 500 ppm, but tremendous recovery was at 50 ppm. Similarly, length of root including hypocotyl exhibited remarkable improvement at 50 ppm as compared to other concentrations after removal of flooding stress. Recovery on 50 ppm significantly improved morphology. Based on morphological results, soybeans were flooded with or without 50 ppm Al2O3 nanoparticles. Abundance of proteins in soybean under flooding stress was mainly related to energy metabolism. However, Al2O3 nanoparticles responsive proteins were predominantly related to protein synthesis / degradation. Moreover, cell death in root including hypocotyl was less obvious with addition of Al2O3 nanoparticles under flooding stress. Furthermore, mRNA and enzymatic analysis were performed to understand the mechanism of recovery from nanoparticles flooding stress. These results suggest that Al2O3 nanoparticles might be helpful to soybean in recovering from flooding stress by regulating its metabolic processes.