The study aimed to compare the physical-chemical attributes of table eggs from three laying hen breeds housed in the cage and cage-free conditions and to characterize the morphological characteristics of the eggshell interior. A morphological and elemental analysis performed by scanning electron microscope coupled with energy dispersive X-ray spectroscopy revealed no abnormalities in the structural integrity of eggshells. The thickness of the eggshell varied in the range from 356.2 to 366.4 µm, with no statistically significant differences between the values. Eggshell membrane thickness was between 20.0 and 59.9 µm, with eggs derived from cage-housed hens, i.e., H/LS/CCE and H/HN/CCE having thinner membrane layers. The results revealed no direct relationships between eggshell and membrane thickness and physical-chemical parameters’ change. However, the presence of thick and long spider-like microcracks on the eggshell surface of eggs from cage-free housed hens H/D/BWE was the main factor that presumably contributed to substantial weight loss during 36 days of egg storage. A noticeable decline in eggshell-breaking strength along with the enlargement of air cells was observed in eggs produced under an enriched cage system H/LS/CCE after 28 days. In contrast, the minor changes in air cell size occurred in eggs from cage-free housed laying hens H/D/BWE. Protein quality indicators such as albumen height and Haugh units were well correlated with each other, and the intensity of their changes during egg storage, to a greater extent, was found to be storage time-dependent. No significant depletion of egg albumen was revealed during the first 15 days of egg storage. According to the United States Department of Agriculture, the quality corresponded to grade A (reasonably firm). However, after 18 days of storage, Haugh unit values were lower than 60, corresponding to grade B (weak and watery). The most apparent reduction in the Haugh unit was observed in eggs produced by enriched cage H/HN/CCE and cage-free H/D/BWE hens. The egg quality was storage time-dependent, and their deterioration rate was primarily associated with the genetic background of laying hens and housing conditions.