Peanuts are a source of proteins and fats but they are also considered a harmful food for individuals who are allergic to them due to their ability to trigger severe and life-threatening reactions. Strict avoidance of peanuts is the most effective means to prevent the development of an allergic reaction. Physical or chemical strategies employing autoclaving can represent a valid alternative to produce a final food with a decreased allergenic power as in the case of peanuts. Thermal processing might induce protein modifications in foods and affect protein digestibility or absorption of nutrients across the intestinal mucosa. Besides, the type of processing could also alter food protein allergenicity thus influencing the interplay with the biological system at the gut level. In this paper, we investigated the influence of autoclaving based treatments on the proliferation of epithelial cells at the intestinal level. Extractable proteins of raw and autoclaved peanuts were analysed by SDS-PAGE and untargeted LC-high resolution-MS/MS to investigate the peptide composition. Our findings show that when raw peanuts were assayed on Caco 2 cell lines, an antiproliferative effect was observed. By contrast, peanuts subjected to hydration and autoclaving did not show an inhibition of proliferation on Caco-2 cells. In parallel, extensive fragmentation induced by autoclaving treatments on the original peanut proteins was also recorded by LC-MS/MS analysis with a consequent increase in the number of peptides detected. These results indicate that the processing applied to peanuts can have an influence on both the nutritional and allergological sides, and more investigations will be required on this issue to understand the alteration of inflammatory mediators induced by the treatment applied.