The presence of mycotoxins in cereals and cereal products remains a significant issue. The use of natural ingredients such as pumpkin and whey, which contain bioactive compounds, could be a strategy to reduce the use of conventional chemical preservatives. The aim of the present work was to study the bioaccessibility of aflatoxin B1 (AFB1) and ochratoxin (OTA) in bread, as well as to evaluate the effect of milk whey (with and without lactic acid bacteria fermentation) and pumpkin on reducing mycotoxins bioaccessibility. Different bread typologies were prepared and subjected to an in vitro digestion model. Gastric and intestinal extracts were analyzed by HPLC-MS/qTOF and mycotoxins bioaccessibility was calculated. All the tested ingredients but one significantly reduced mycotoxin intestinal bioaccessibility. Pumpkin powder demonstrated to be the most effective ingredient showing significant reductions of AFB1 and OTA bioaccessibility up to 74% and 34%, respectively. Whey, fermented whey, and the combination of pumpkin-fermented whey showed intestinal bioaccessibility reductions between 57-68% for AFB1, and between 11-20% for OTA. These results pointed to pumpkin and milk whey as potential bioactive ingredients that may have promising applications in the bakery industry.