The production of soy protein-based foods requires multiple-step, intensive processing and storage of soy ingredients, which can increase the product's susceptibility to oxidation. Therefore, we investigated the oxidative stability of soy protein-based products subjected to different relevant conditions or treatments: over storage of soy flours, over fractionation to yield soy protein isolate (SPI), and over subsequent thermomechanical processing to yield a model structured product. Soy flours were stable to lipid and protein oxidation over 250 days storage in chilled or ambient conditions. The fractionation process applied to make SPI did not increase substantially protein carbonylation, but increased surface-exposed hydrophobicity and decreased free thiols, compared to the starting defatted flour. Subsequent processing of hydrated SPI powder at 140 °C further increased protein carbonylation to a high extent. Therefore, we conclude that soy flours can be stable over long storage times, but processing to yield structured foods products promote protein oxidation.