Ethanol extracts (EE) from fenugreek and quinoa seeds with different total content of inhibitory compounds (TIC, total saponin plus phenolic) were prepared with and without concentration of TIC (CEE -concentrated EE-, and EE, respectively). Their inhibitory activity on pancreatic lipase and α-amylase was assessed by traditional in vitro methods (with or without orbital shaking), and by simulating intestinal digestion. CEE contained higher contents of TIC than EE, being fenugreek superior to quinoa (p < 0.001). The extracts inhibited enzymes in a dose-dependent manner, CEE extracts being stronger (fenugreek for lipase -p = 0.009-, and quinoa for α-amylase -p < 0.001-). Shaking did not impact the activity. Intestinal conditions worsened the inhibition of lipase, but slightly catalyzed the α-amylase. Longer times of reaction worsened activities. The importance of assessing the inhibitory activity of extracts under simulated intestinal conditions is concluded, being fenugreek more interesting than quinoa, especially against pancreatic lipase.