Hard to cook is a textural defect that affects the nutritional quality of beans stored under adverse temperature and humidity conditions. This defect is related to intrinsic characteristics such as seed coat thickness, composition and microstructure. The aim of the present study was to evaluate the chemical and microstructural characteristics of common bean (Phaseolus vulgaris L.) during 270 days of post-harvest storage at 30 °C and 70% relative humidity. Microstructural analysis revealed alteration of the cotyledon cell wall and seed coat affecting seed viability and restricting seedling emergence. The seed coat thickness contraction from 105.79 μm to 97.35 μm (270 days). Changes are related with the protein bodies migration from cotyledons to seed coat. An increase in neutral detergent fiber and the presence of CaOx crystals were observed, which confer rigidity to the seed coat and affect water diffusion after 150 days causing permeability changes that contributed to seed hardening.