Four common bean (Phaseolus vulgaris L.) varieties, Kawanda (K)131, K132, NABE4 and NABE11, were evaluated for the relationship between development of the hard-to-cook (HTC) defect and changes in nutritional quality during 6-month storage under ambient conditions. All varieties developed the HTC defect, but the extent was found to vary with variety. Cooking time increased by 113% in K131, 95.3% in K132, 56.4% in NABE4 and 42.93% in NABE11 after 6 months. The development of the HTC defect was found to be associated with a reduction in phytic acid content (r2 = -0.802), in vitro protein digestibility (r2 = -0.872) and in vitro starch digestibility (r2 = -0.729). The susceptibility to the HTC defect during storage could be attributed to a phytic acid interaction with proteins and carbohydrates, and is also associated with small seed size. Breeding for large seed size could therefore help reduce the development of the HTC defect.