Soybean is oil and protein rich legume crop that exhibits markedly reduced growth and yields under flooding stress. The abundances of four proteins changed significantly during post-flooding recovery were investigated at enzyme activity level using organ-specific and stress-specific enzyme assays. Peroxidase was decreased under flooding and cold stresses and was increasing during recovery stage. However, it was increasing under drought stress in both root and hypocotyl. Haloacid dehalogenase-acid phosphatase was suppressed in root under flooding and cold stresses and slightly increased during recovery; however, opposite pattern revealed in hypocotyl. Drought did not change the activity in root, but decreased in hypocotyl. The beta-ketoacyl reductase did not change under flooding in root; however, it was decreased in hypocotyl and increased slightly during recovery stage. It was decreased under drought and cold stresses but trended towards increase during the recovery stage in both organs. Nucleotidylyl transferase was increased under flooding and drought stresses in root, but decreased in hypocotyl. It was decreased by cold treatment that slightly increased during recovery stage. Furthermore, jasmonate and salicylate suppressed the activities of peroxidase and haloacid dehalogenase-acid phosphatase under flooding stress in both organs; however acid phosphatse increased during recovery. Beta-ketoacyl reductase and nucleotidylyl transferase were elevated by jasmonate in root under flooding and decreased progressively during recovery. These results suggest that jasmonate associated changes in enzyme activities might facilitate soybean root recovery after flooding stress.