Soybean is an important food crop containing abundant protein and vegetable oil [1]. Soybean is unique among crops, because it supplies protein equal in quality to that of animal sources [2]. Soybean is advantageous for biodiesel producing, which is converted from vegetable oil, because it is produced without or nearly zero nitrogen [3]. In addition, soybean is rich in phytochemicals such as isoflavones and phenolic compounds [4], which contributed to reducing the risk of heart/ cardiovascular diseases, osteoporosis, and cancer [5]. Furthermore, it is possible for soybean to step into symbiosis with rhizobia to provide nitrogen for plant growth and development [6]. These findings document several aspects of soybean, including nutritional elements, biodiesel production, pharmacological values, and symbiosis potential. Soybean production is affected by abiotic constraints, including weather-related phenomena, soil-nutrient availability, salinity, and photoperiod [2]. Annual global losses in crop production due to flooding are comparable to those caused by drought [7]. Flooding is composed of several underlying changes such as oxygen, carbon dioxide, reactive oxygen species (ROS), and phytotoxins inside plants and from environment [8]. Due to restricted gas exchange, deficit of energy/carbohydrate and accumulation of volatile ethylene occurred by flooding [9]. Drought poses as another constraint for plant growth and terrestrial ecosystem productivity [10]. Drought induced meristematic cells, reduced cell division [11], and limited cell elongation/expansion growth [12]. These findings indicate that flooding and drought are complex abiotic stressors affecting plant growth. A series of findings were obtained in soybean with different exposure time to flooding and drought stresses using proteomic techniques (Fig. 1). With flooding duration, a plethora of biological processes underwent, including signal transduction, hormone regulation, transcriptional control, glucose degradation, sucrose accumulation, alcoholic fermentation, mitochondrial impairment, proteasome-mediated proteolysis, and cell wall loosening [13]. Signal transduction of calcium [14] and hormone regulation of abscisic acid [15] as well as gibberellic acid [16] were activated by flooding. Moreover, fermentation [17] as well as gamma-aminobutyric acid shunt [18] were induced in flooded soybean. As reported, lignification [19] and electron transport chains [18] were altered; however, ROS scavenging [19] and protein glycosylation [20] were suppressed. Regarding post-flooding recovery, scavenging of toxic radicals [21], ATP generation/secondary metabolism [22], and cell wall metabolism/cytoskeleton reorganization [23] were responsible for recovery. These findings indicate that different strategies might be utilized in soybean under flooding conditions and during post-flooding recovery stage.