Beans (Phaseolus vulgaris L.) contain nutritional and functional compounds, and form a staple diet for approximately one-third of the population worldwide. Due to the seasonal production of beans, the grains need to be stored for the off-season, and, in general, quality losses are observed. Among the main property changes, changes in color and cooking properties are easily perceived. Therefore, the storage conditions that prevent (low temperature and vacuum) and that favor (room temperature and absence of vacuum) the occurrence of these changes was studied to better understand the possible causative modifications and alterations in the proteomic profile of beans. The best storage condition involved the combination of low temperatures with vacuum; however, with one year of storage at this condition, a loss of quality with respect to coloration, cooking property and protein profile was observed. •Nutritionally important proteins are affected during bean storage.•Vacuum storage does not maintain the nutritional characteristics of common beans.•The common beans, there is a loss of quality such as coloration, cooking property and protein profile during storage.