Bread crust constitutes an important by-product of the bakery industry, and its utilization for the isolation of melanoidins to be used as a functional ingredient can enhance its added value and contribute to health. The aim of this study was to evaluate the bioaccessibility, bioactivity, and genoprotective effect of melanoidins derived from bread crust. Bioaccessibility was assessed in gastric, intestinal digestion, and colonic fermentation fractions. The results revealed a relationship between bioaccessible melanoidins and their type (common or soft bread). No cytotoxicity effects were observed for bioaccessible fractions, as assessed by MTT and RTA methods, and they did not affect the distribution of E-cadherin in Caco-2 cells, confirming their ability to maintain membrane integrity. Furthermore, our study demonstrated that the gastrointestinal and colonic fermentation fractions successfully transported across the intestinal barrier, without affecting cell permeability, and showed antioxidant activity on the basolateral side of the cell monolayer. Remarkably, both fractions displayed a significant genoprotective effect in Caco-2 cells. Our findings provide crucial insights into the relationship between the melanoidins and their bioactivity and genoprotective effect. These results demonstrated the potential of bioaccessible melanoidins as valuable bioactive compounds for the development of functional foods, without showing toxic effects on gastrointestinal cells.