Previous studies have related the slow digestion properties of isolated starches with their amylose to amylopectin ratio as well as their molecular structure, and in the case of flours, with their accompanying components such as proteins and fibers; which are known to restrict, to different extents the starch digestion by amylolytic enzymes. However, the botanical origin as well as the internal architecture of native starch granules plays a significant role in these characteristics. Moreover, these features can be improved by using hydrothermal treatments, such as heat moisture treatment (HMT) and annealing (ANN), that promote changes to granular architecture, increase internal crystallite order and decrease the amount of amorphous zones. In this study, HMT and ANN treated starches from two bean varieties and a normal maize starch are analyzed in terms of thermal stability, assessed by differential scanning calorimetry, viscosity by rapid visco analysis and in vitro amylolysis. The HMT and ANN treatments promote lower hydrolysis when compared to native granules, due to new and/or improved molecular interactions between starch molecules, assessed by attenuated total reflectance‐fourier transform infra red spectroscopy; such interactions increase the amount of crystalline residues after digestion, which is related with lower water absorption during cooking, and enhanced thermal stability, despite the lower enthalpies in thermal treated starches (≈3 J g−1 in Black bean with HMT). Furthermore, the hydrolysis residues after 120 min of amylolysis present a higher ratio of crystalline regions, that improve with thermal treatments, this demonstrates that these processes increase the order of existing crystallites due to new molecular interactions among starch molecules.