The bioaccessibility of total flavonoids, catechin, epigallocatechin, epigallocatechin gallate, epicatechin, rutin, quercetin, isoquercetin, and kaempferol, and changes in antioxidant activities in fresh and mature fava bean seeds during simulating gastrointestinal conditions has been investigated. The portion of bioaccessible flavonoids potentially available for further uptake varies between pods. Flavonoids of mature and fresh seeds after the gastric phase, intestinal phase, and dialysable fraction, simulating bioaccessible flavonoids, were 6.62% and 1.78%, respectively, compared with no-digested pods. Total antioxidant capacities in the bioaccessible fractions were significantly lower than the control. Furthermore, potential bioactivity as a PPAR-gamma antagonist was evaluated, where epigallocatechin gallate presents at -9.50 Kcal/mol vs. -6.53 Kcal/mol, present in troglitazone. These results highlighted that gastrointestinal digestion may substantially affect the absorption of flavonoids in mature and green fava beans and present a potential bioactivity against obesity.