The changes in components and biological activities of doenjang samples prepared with black soybeans and fermented with Bacillus subtilis SCB were investigated. The amino nitrogen (A-N) contents of samples increased with increasing black soybean content. A doenjang product made using a 1:1 ratio of soybeans-black soybeans showed a maximum level of genistein and daidzein isoflavones ($1111.6{mu}g/g$) at 110 days of fermentation, along with decreasing contents of genistin and daidzin due to the conversion to aglycones. The black soybean-only doenjang sample showed higher protease activity, including caseinolytic and fibrinolytic enzyme activities, than the other samples, and had relatively higher polyphenol content and DPPH radical scavenging activity. Therefore, doenjang made with additions of black soybeans and fermented by B. subtilis SCB may have improved physiological properties, suggesting this to be a valuable method of preparation.