Hens of the laying hybrid ISA Brown were used in the study with the objective to evaluate eggshell quality, microbial contamination of eggshells, and penetration of microorganisms into the egg content in different housing systems (enriched cage: 60 hens, 10 hens per cage, 750 cm2 per hen vs free range: 60 hens, 9 hens per m2) and at different hen ages (26 vs 51 weeks) during storage time (0, 2, 7, 14, and 21 days). A significant interaction between the housing system and age was observed in egg weight and most of eggshell quality measurements. However, microbial contamination and penetration were affected mostly by the housing system and storage time. The numbers of Escherichia coli (P < 0.001, 4.51 vs 2.75 log cfu/eggshell) and Enterococcus (P < 0.001, 2.56 vs 1.11 log cfu/eggshell), and the total number of microorganisms (P < 0.001, 5.04 vs. 3.65 log cfu/eggshell) were higher in free range eggs compared to enriched cage eggs, respectively. The counts of Escherichia coli (P < 0.001, 4.23 vs 2.91 log cfu/eggshell) and Enterococcus (P < 0.001, 2.31 vs 1.27 log cfu/eggshell) decreased with storage time. A positive correlation between the total number of pores and penetration of Escherichia coli in both housing systems was observed in the albumen. It can be concluded that the housing system and age of laying hens significantly affected eggshell quality. Microbial contamination presumably affects the penetration of microorganisms. The correlation between the number of pores and penetration is assumed to be affected by the microbial species.