Time-dependent primary and secondary metabolite changes of soybean contaminated with Aspergillus sojae and their associations were discussed. Partial least squares discriminant analysis showed that the patterns of fungus infected soybean were clearly distinguished from untreated samples based on its time intervals. A. sojae depends on soybean for its carbon source resulting gradual decrease in the glucose, fructose and myo-inositol levels. The stimulation in l-phenylalanine by A. sojae increases the accumulation of naringenin from days 1 to 6, leading to the changes in genistein pool. Even though the level of glucosides like daidzin, genistin and glycitin decreased during treatment, other isoflavones and coumestan levels enhanced. Due to the increase in glycinol, the resulting phytoalexins such as glyceollin I and glyceollin II augmented by fungal treatment. The changes in secondary metabolites reflects in total phenolic content and because of the increase in glyceollin I, II and glyceofuran reflect their radical scavenging capacity; A. sojae-mediated soybean registered a periodic increase in the radical scavenging activity.