Previously, Fermalogic proposed the idea of recovering isoflavones as co-products from soy-based industrial fermentations such as the Saccharopolyspora erythraea erythromycin fermentation. Unfortunately, soy isoflavones are extensively biotransformed and/or degraded during the fermentation process making the process commercially impractical due to the low yield of isoflavones. During the current study the chemical structures of the isoflavone biotransformation products were determined which suggested a method for blocking isoflavone metabolism through inactivation of the genes coding for their biotransforming enzymes. Ultimately the pathway blocking approach proved to be unsuccessful and an alternative strategy was developed which will be presented and which is now ready for commercial development.