In the present research, effect of sequential addition of Bifidobacterium bifidum, Bacillus subtilis and Rhizopus oligosporus on content and composition of vitamin K 2 and isoflavones in fermented soy foods have been investigated. Initially, soybeans were fermented with B. bifidum; then this fermented mass was re-fermented with co-culture of B. subtilis and R. oligosporus. The evolved sequence of microbes inoculation tended towards significantly (p <0.5) higher enzymes levels (126.16±2.23 IU/mg lipase, 36.52± 1.25 IU/mg phytase and 8.52±1.12 IU/mg β-glucosidase); maximum menaquinone-7 production (9.3±1.27 μg/g); and isoflavone content (84.64±1.97 % daidzein, 99.29±0.86 % genistein, 96.42±1.32 % glycitein) after 72 h of solid-state fermentation. The study showed that co-fermentation of soybean with different microbes in a particular sequence can enhance nutritional value batter than the mono-culture fermentation due to the positive correlation between enzymes (lipase, phytase, β-glucosidase) levels, menaquinone-7 and soy isoflavones content.