Soy has been traditionally incorporated in diet as processed foods, such as soymilk, tofu, miso, tempeh, etc., and the consumption is commonly associated with a reduction of the development of chronic diseases due to their antioxidant, anti-inflammatory, and anti-allergic properties, among others. Many of the health benefits of soy have been attributed to isoflavones. They comprise a group of naturally occurring flavonoids consisting of heterocyclic phenols. Soy contains three types of isoflavones in four chemical forms: the aglycones daidzein, genistein, and glycitein; the β-glucosides daidzin, genistin, and glycitin; their 6″-O-malonyl-β-glucosides (6OMalGlc); and their 6″-O-acetyl-β-glucosides (6OAcGlc) conjugates. Industrial processing methods of soy-based food products commonly lead to the loss of isoflavones through removal of undesirable fractions. On the other hand, isoflavones can be transformed into different conjugates, which may have significant effects on the food texture and on the bioavailability and pharmacokinetics of the isoflavones. This article reviews the effect of a number of soybean processing treatments on the isoflavone content and profile. The preparation and manufacturing of different soy-based food and food ingredients, fermented and non-fermented, has been analyzed in terms of content and distribution of the three major isoflavone derivatives, daidzein, genistein, and glycitein, and their respective conjugates.