Saponin-rich extracts from edible seeds have gained increasing interest and their hydrolysis to sapogenin-rich extracts may be an effective strategy to enhance their potential bioactivity. However, it remains necessary to study the resulting chemical modifications of the extracts after hydrolysis as well as their impact on the subsequent bioaccessibility of bioactive compounds. The chemical composition of non-hydrolyzed and hydrolyzed extracts from fenugreek (FE, HFE) and quinoa (QE, HQE), and the bioaccessibility of saponins, sapogenins and other bioactive compounds after an in vitro gastrointestinal digestion was assessed. In general, FE mainly contained saponins (31%), amino acids (6%) and glycerides (5.9%), followed by carbohydrates (3.4%), fatty acids (FFA) (2.3%), phytosterols (0.8%), tocols (0.1%) and phenolics (0.05%). HFE consisted of FFA (35%), sapogenins (8%) and partial glycerides (7%), and were richer in phytosterols (1.9%) and tocols (0.3%). QE mainly contained glycerides (33%), FFA (19%), carbohydrates (16%) and saponins (7.9%), and to a lesser extent alkylresorcinols (1.8%), phytosterols (1.5%), amino acids (1.1%), tocols (0.5%) and phenolics (0.5%). HQE mainly consisted of FFA (57%), partial glycerides (23%) and sapogenins (5.4%), were richer in phytosterols (2.4%), phenolics (1.2%) and tocols (0.7%) but poorer in alkylresorcinols (1%). After in vitro digestion, saponins from FE and QE were fully bioaccessible, sapogenins from HFE displayed a good bioaccessibility (76%) and the sapogenin from HQE was moderately bioaccesible (38%). Digestion of saponin and sapogenin standards suggested that other components of the extracts were enhancing the bioaccessibility. Other minor bioactive compounds (phytosterols, alkylresorcinols, tocols and some phenolics) also displayed optimal bioaccessibility values (70–100%).