In this study, the transepithelial transport of bioactive peptides derived from faba bean flour gastrointestinal digestates was investigated, in vitro, using a Caco-2 and HT29-MTX-E12 coculture monolayer, in comparison to those of pea and soy. The profile of transported peptides was determined by mass spectrometry, and the residual antioxidant activity was assessed. The ORAC value significantly (p < 0.05) decreased after transepithelial transport (24-36% reduction) for all legumes, while the antioxidant activity in ABTS assay significantly (p < 0.05) increased, as shown by the EC50 decrease of 26-44%. Five of the nine faba bean peptides that crossed the intestinal cell monolayer exhibited antioxidant activity. Two of these peptides, TETWNPNHPEL and TETWNPNHPE, were further hydrolyzed by the cells' brush border peptidases to smaller fragments TETWNPNHP and TWNPNHPE. These metabolized peptides were synthesized, and both maintained high antioxidant activity in both ABTS (EC50 of 1.2 ± 0.2 and 0.4 ± 0.1 mM, respectively) and ORAC (2.5 ± 0.1 and 3.4 ± 0.2 mM of Trolox equivalent/mM, respectively) assays. These results demonstrated for the first time the bioaccessibility of faba bean peptides produced after in vitro gastrointestinal digestion and how their bioactive properties can be modulated during transepithelial transport.