The aim of this study was to evaluate the impact of the genotype (guinea fowl, native breed Leghorn, and commercial hybrid hens), storage time (0, 14, 28 d) and storage temperature (fresh, 5, 20°C) on eggshell quality traits and microbiological contamination of eggshell, eggshell membranes, and albumen. A total of 150 hens (50 hens per genotype—divided into 2 equal groups because of the results replication) were used. There were 150 eggs (50 per genotype) used for microbial analysis and 600 eggs used for the analysis of eggshell quality. The effects of genotype, storage time, and storage temperature were observed. Moreover, interactions between these factors were calculated. The significant effect of genotype (P = 0.0001) was found in egg weight, in all observed parameters of eggshell quality (proportion, thickness, strength, surface, and index), eggshell contamination of Escherichia coli (EC) and total number of micro-organisms (TNM), penetration of TNM into eggshell membranes (P = 0.0014), and penetration of TNM into albumen (P = 0.0019). Storage time significantly affected egg weight and all parameters of eggshell quality except the eggshell strength and index. It also significantly affected count of Enterococcus (ENT) on eggshell, TNM in eggshell membranes and TNM in albumen. Storage temperature significantly influenced egg weight (P = 0.0001) and all parameters but eggshell thickness and surface. Regarding the microbial contamination, storage temperature significantly affected a count of ENT on shell, TNM in shell membranes, and TNM in albumen. Concerning significant interactions, the interaction among genotype and storage time was found significant (P = 0.0148). Fresh and 28-day-old commercial hybrid eggs were the most contaminated, whereas guinea fowl eggs (fresh and 14 d old) and Leghorn hen eggs (fresh, 14, 28 d old) had the lowest level of contamination by EC. When looking for an alternative to laying hens, guinea fowls should be taken into consideration due to their higher resistance to diseases, ability of adaptation to different environmental conditions, and especially in terms of eggshell quality and therefore egg safety.