Lentils are sustainable sources of bioencapsulated macronutrients, meaning physical barriers hinder the permeation of digestive enzymes into cotyledon cells, slowing down macronutrient digestion. While lentils are typically consumed as cooked seeds, insights into the effect of cooking time on microstructural and related digestive properties are lacking. Therefore, the effect of cooking time (15, 30, or 60 min) on in vitro amylolysis and proteolysis kinetics of lentil seeds (CL) and an important microstructural fraction, i.e., cotyledon cells isolated thereof (ICC), were studied. For ICC, cooking time had no significant effect on amylolysis kinetics, while small but significant differences in proteolysis were observed (p < 0.05). In contrast, cooking time importantly affected the microstructure obtained upon the mechanical disintegration of whole lentils, resulting in significantly different digestion kinetics. Upon long cooking times (60 min), digestion kinetics approached those of ICC since mechanical disintegration yielded a high fraction of individual cotyledon cells (67 g/100 g dry matter). However, cooked lentils with a short cooking time (15 min) showed significantly slower amylolysis with a lower final extent (~30%), due to the presence of more cell clusters upon disintegration. In conclusion, cooking time can be used to obtain distinct microstructures and digestive functionalities with perspectives for household and industrial preparation.