This study evaluated the external and internal quality characteristics after various storage periods (SP) of eggs from different management practices (MP) regarding layer hen housing and feeding systems. One hundred eggs collected from farms with Lohman Sandy hens raised in i) a cage system where the standard diet was offered ad libitum (CAB), ii) a free-range production system with free access to both the standard diet and alfalfa pasture for grazing (FRG), or iii) a village poultry system where hens were fed on insects, grass, vegetables, or kitchen waste, as well as a restricted standard diet (VCR) were stored at 0, 7, 14, 21, and 28 d at +4 °C and 60% relative humidity. Data were analysed in a three MP × five SP factorial arrangement with 20 eggs each. SP was analysed using polynomial regression. The CAB eggs had a higher weight loss and shell ratio compared to the FRG and VCR eggs. The yolk index, albumen index, Haugh unit (HU), and yolk colour of FRG and VCR eggs were higher than CAB eggs. The yolk ratio of the CAB group was higher than that of the other groups, whereas the albumen ratio was lower. The egg weight loss increased linearly, whereas the albumen ratio and pH increased cubically during storage. The egg weight loss, shell thickness, and yolk index were related to the interaction between MP and SP. Shell ratio and all internal quality traits, except for the pH of yolk and albumen, reflected only the effect of the MP; the association became more significant as the SP increased. Our results suggest that shell ratio, surface area, and all internal quality traits, except for yolk colour, change during storage.