Peptides released from gluten proteins during gastrointestinal digestion can trigger various wheat-related disorders, including celiac disease (CeD), wheat allergy, and wheat allergy dependent on augmentation factors (WALDA). Our study aimed to identify and quantify these immunoreactive peptides (IPs) in relation to gluten digestibility. We compared the gluten digestibility of different cereals and examined its temperature-dependent impact. Wheat, rye, and barley flours, along with their yeast-leavened and sourdough-fermented breads, were subjected to simulated in vitro gastrointestinal digestion following the INFOGEST protocol. The resulting peptides were identified and relatively quantified using nano liquid chromatography coupled with tandem mass spectrometry. The residual gluten peptide content in the digesta was measured using an enzyme-linked immunosorbent assay. No differences in digestibility were observed between white wheat flour and whole grain flour. Among the three cereals, barley flour had the lowest digestibility, while wheat flour had the highest, based on average peptide sequence length and gluten content of the digesta. We identified 569 IPs in wheat flour digesta, compared to only 388 IPs found in rye and barley samples, respectively. For wheat and barley, most IPs were linked to CeD, whereas rye showed equal abundance of IPs associated with both CeD and WALDA. A comparison of digestibility between bread crust and crumb revealed that higher temperatures, as reached in the crust, reduced gluten digestibility and increased IP abundance. Furthermore, the gluten digestibility of the crumb was higher than that of the flour, indicating that the bread-making process positively affected digestibility.