Plant hormones play a critical role in the physiological and biochemical mechanisms of plants, with functions such as regulating the metabolic pathways of secondary metabolite production and alleviating external stresses. In this study, the synthesis of flavonoids in black soybean sprouts was induced by slight acid combined with the plant hormones abscisic acid (ABA) and melatonin (MT). The results indicated that the contents of daidzin, genistin, daidzein, and genistein in black soybean sprouts treated with slight acid were increased by 10 μM ABA and 75 μM MT, and the total flavonoid content was significantly enhanced. Compared with the slight acid treatment, the H2O2 and malondialdehyde (MDA) contents in black soybean sprouts were increased after ABA treatment, and the black soybean sprouts were further stressed. However, the H2O2 and MDA contents in black soybean sprouts were significantly decreased after MT treatment, indicating that the stress of black soybean sprouts can be alleviated by MT. Under slight acid stress, the genes related to flavonoid synthesis in black soybean sprouts were induced by exogenous ABA, promoting the accumulation of flavonoids; under exogenous MT treatment, the activity of phenylpropanoid metabolism enzymes was significantly increased, the genes related to flavonoid synthesis were upregulated, and flavonoid synthesis was induced. These results suggest that the combination of slight acid and plant hormone treatments promotes the accumulation of flavonoid substances during the germination of black soybeans. This research lays the foundation for improving the growth conditions of black soybeans and promoting the enrichment of flavonoid substances in black soybeans.