Isoflavones are major phenolic compounds found in soybeans and soy-based foods. Health-beneficial functions of soy foods are closely associated with these phytoestrogenic compounds. Twelve chemical forms of isoflavones are found in soybeans including three aglycones (genistein, daidzein, and glycitein), and their corresponding conjugated ${eta}$-glucosides, 6"-$O$-acetyl-${eta}$-glucosides, or 6"-$O$-malonyl-${eta}$-glucosides. Distributions of isoflavones in soy foods are dependent on the processing conditions especially the applied thermal energy and moisture contents. Conventional thermal treatment with high moisture and at temperature lower than 100, such as boiling and cooking, transforms 6"-$O$-malonyl-${eta}$-derivatives into ${eta}$-glucosides via intra-conversion. Dry heat treatment with limited moisture contents such as frying, toasting, baking, explosive puffing, and roasting process increases the formation of 6"-$O$-acetyl-${eta}$-derivatives of isoflavones through decarboxylation from 6"-$O$-malonyl-${eta}$-derivatives. Fermentation with microorganisms or natural products containing high ${eta}$-glucosidase activity can produce aglycones from ${eta}$-glucosides in soy foods. New isoflavone metabolites such as 6"-$O$-succinyl daidzin and 6"-$O$-succinyl genistin are found in soy-fermented foods with Bacillus species. Major precursors for the generation of these succinyl isoflavones in Bacillus-fermented soy foods are ${eta}$-glucosides rather than aglycones. Riboflavin photosensitization can decrease the stability of isoflavones greatly in model systems and soymilk, which implies that isoflavones in soy foods require proper protection from light exposure to maintain its functional properties in foods. This review was aimed to provide comprehensive understanding on the transformation of isoflavones in soy foods treated with diverse processing methods including thermal treatments, fermentation using natural compounds, microorganisms, and photosensitization.