The effects of processing techniques on the distribution of isoflavones were investigated by manufacturing tempeh, soymilk, tofu, and protein isolate. The manufacturing steps causing significant losses (p < 0.05) of isoflavones were as follows: soaking (12%) and heat processing (49%) in tempeh production; coagulation (44%) in tofu processing; and alkaline extraction (53%) in soy protein isolate production. In the production of tempeh, soymilk, and tofu, malonyldaidzin and malonylgenistin decreased after soaking and cooking. Concomitantly, acetyldaidzin and acetyl-genistin were generated during heat processing. After fermentation, daidzein and genistein concentrations increased in tempeh, apparently as a result of fungal enzymatic hydrolysis. In protein isolate processing, alkaline extraction caused the generation of daidzein and genistein, probably through alkaline hydrolysis.