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Cotyledon cells in kidney beans naturally encapsulate starch and proteins limiting the access of digestive enzymes to their substrates. In this study, we investigated the effect of cell wall on bean protein digestibility and its relationship with starch digestion. Results showed that proteins contained in the cytoplasmic matrix influence the rate at which starch is digested in-vitro. Confocal laser scanning microscopy revealed that storage proteins in the cytoplasm act as a second encapsulation system preventing starch digestion. This microstructural organization only affected starch since no changes in protein digestion rate or extent were observed due to the presence of starch granules. Fourier transform infrared spectroscopy revealed that cellular entrapment limited protein denaturation induced by thermal treatments. High concentrations of a fraction resistant to digestion were found in proteins that were heated when entrapped within intact cotyledon cells, compared to those thermally treated as bean flour.