Microwave cooking of legumes such as chickpeas and common beans was evaluated by assessing the cooking quality (cooking time, firmness, cooking losses, and water uptake) and the physicochemical, nutritional, and microstructural modifications in starch and nonstarch polysaccharides. Compared to conventional cooking, microwave cooking with sealed vessels enabled a drastic reduction in cooking time, from 110 to 11 min for chickpeas and from 55 to 9 min for common beans. The solid losses, released in the cooking water, were significantly less after microwave cooking than after conventional cooking (6.5 vs 10.6 g/100 g of dry seed in chickpeas and 4.5 vs 7.5 g/100 g of dry seed in common beans). Both cooking procedures produced a redistribution of the insoluble nonstarch polysaccharides to soluble fraction, although the total nonstarch polysaccharides were not affected. Increases in in vitro starch digestibility were similar after both cooking processes, since the level of resistant starch decreased from 27.2 and 32.5% of total starch in raw chickpeas and beans, respectively, to about 10% in cooked samples and the level of rapidly digestible starch increased from 35.6 and 27.5% to about 80%. SEM studies showed that the cotyledons maintained a regular structure although most of the cell wall was broken down and shattered by both cooking procedures. In addition, the ultrastructural modifications in the cotyledon's parenchima and cells are consistent with the chemical modifications in NSP and the increase in starch digestibility after cooking.