Time dependent changes of primary (GC–MS), isoflavones (LC–MS) and minerals (ICP-OES) content of fermented soya-chunk were compared with un-fermented (0H) soya-chunk and presented. Results revealed that the amino acid content increased gradually based on the fermentation time; whereas the maltose, sucrose and fructose contents were reduced due to the fungal growth. The glucosides changed extensively during the initial fermentation time resulting in augmentation of aglycones and phytoalexins. This affects the antioxidant potential whereas the DPPH and ABTS of 0H showed lowest activity (18.15% and 54.92%) and increased quite high with fungal fermentation (45.81% and 93.47%). The calcium (0.55%), magnesium (0.47 mg/kg), nickel (5.17 mg/kg l−1), and copper (8.33 mg/kg l−1) content were increased during the fermentation and in a decrease of iron and aluminium contents. Findings suggest that the soya-chunk prepared by fungal fermentation will improve the antioxidant and mineral content and hence their nutritional property will be enhanced for humans.