The objective of this work was to evaluate the effects the solid-state fermentation parameters of defatted soybean flour (DSF) by Monascus purpureus or Aspergillus oryzae on the bioactive compounds. Central composite rotatable design, multi-response optimization, and Pearson's correlation were used. The fermentation parameters as initial pH (X1), DSF-to-water ratio (X2), and incubation temperature (X3) were taken as independent variables. The function responses were isoflavone content, total phenolic content (TPC), and antioxidant activity. All fermentation parameters affected the isoflavone content when fermented by Monascus purpureus, whereas the TPC or antioxidant activities remained almost unchanged. For the fermentation by Aspergillus oryzae, all the function responses were influenced by X2 and X3 and were independent of the X1. Estimated optimum conditions were found as x1 = 6.0, x2 = 1:1, and x3 = 30 °C for both fungi. Achieving suitable fermentation parameters is essential to increase bioactive compounds in the DSF that makes it promising for food industrial applications.