Raffinose oligosaccharides (ROs) make up a substantial part (40%) of the soluble sugars found in soybean seeds and are responsible for flatulence after the ingestion of soybean and other legumes. Consequently, soy-based foods would find a broader approval if the ROs were removed from soybean products or hydrolysed by α-galactosidases. During soybean seed germination, of content the ROs decrease substantially, while the α-galactosidase activity increases. α-Galactosidase was partially purified from germinating seeds by partition in an aqueous two-phase system and ion-exchange chromatography. The enzyme preparation presented maximal activities against ρ-nitrophenyl-α-d-galactopyranoside (ρNPGal) at 60 °C and a pH of 5.0 and the KM app values for ρNPGal, melibiose, and raffinose of the enzyme preparation were 0.33, 0.42, and 6.01 mM, respectively. The enzyme was highly inhibited by SDS, copper, and galactose. Hydrolysis of soybean flour ROs by enzyme preparation reduced the stachyose and raffinose contents by 72.3% and 89.2%, respectively, after incubation for 6 h at 40 °C.