Rice and wheat steamed bread are common staple foods and important protein sources in the human diet. They are often prepared and refrigerated for later consumption. Here, we explored the influences of refrigeration on protein oxidation in rice and wheat steamed bread and investigated the effects of the resulting oxidized proteins on the human gut microbiota using an in vitro fermentation model. We found that as refrigeration time increased, the levels of protein oxidation products, including carbonyl groups and advanced glycation end products, in rice and wheat steamed bread increased, whereas those of free sulfhydryl and free amino groups decreased. The levels of specific amino acids (tyrosine, tryptophan, and glutamic acid) decreased with refrigeration, whereas those of amino acid oxidation products (dityrosine, N′-formylkynurenine, and kynurenine) increased. Furthermore, the relative abundance of potentially harmful bacteria, particularly Sutterella and Tyzzerella, increased, whereas that of probiotics, particularly Bifidobacterium and Phascolarctobacterium, decreased when rice and steamed bread proteins subjected to different refrigeration times were fermented with human gut microbiota. Moreover, the concentrations of short-chain fatty acids (acetate, propionate, and butyrate) in fermentation broth decreased with refrigeration. The results demonstrated that the degree of protein oxidation increased with refrigeration time, and the consumption of these oxidized proteins may disrupt gut microbiota composition and increase the risk of chronic inflammation. Therefore, cooked rice and wheat steamed bread should be eaten immediately or kept refrigerated for as short a time as possible.