Studies on the physico-chemical, microstructural characteristics and in vitro (under simulated gastric and small intestine conditions) starch digestibility of navy beans were carried out. The microstructure of raw and cooked beans observed through scanning electron microscopy (SEM) showed the presence of hexagonal or angular shaped cotyledon cells (50–100 μm size) containing starch granules with a size ranging between 10 and 50 μm. The extent of starch hydrolysis (%) after 120 min of in vitro gastro-intestinal digestion differed between whole navy beans (∼60%) and milled bean flour and bean starch (85–90%) after they were cooked under similar conditions. Starch hydrolysis (%) increased significantly when the cotyledon cells in the cooked whole navy beans were disrupted using high pressure treatment (French press). The storage of freshly cooked whole beans resulted in a lower (40–45%) starch hydrolysis whereas re-heating increased the same to 70–80% during in vitro small intestinal digestion. The SEM pictures of cooked navy bean digesta after different intervals of in vitro gastric and small intestinal digestion showed that the cotyledon cell structure is maintained well throughout the digestion period. However cotyledon cells appear shrunken and developed wrinkles during in vitro digestion. Particle size analysis of cooked bean paste taken before and after the in vitro gastro-intestinal digestion showed similar particle size distributions.