In this study we investigated the change in antigenicity and allergenicity of Meju, a traditional Korean soybean product, by fermentation via 3 different microorganisms. The steamed soybeans were fermented with Lactococcus lactis subsp. lactis and/or Aspergillus oryzae and/or Bacillus subtilis. Proteins in soybean were degraded after fermentation. Antigenicity or allergenicity were analysed by immunoblotting and ELISA using soybean protein-specific polyclonal antibodies or soybean allergic patient sera. The best degradation was achieved by three step fermentation using nisin-producing Lactococcus lactis subsp. lactis IFO12007, A. oryzae and B. subtilis. Allergenicity and antigenicity were also starkly reduced after three step fermentation. The three-step fermentation method developed in our lab suggests an excellent alternative to reduce the allergenicity of soybeans.