The aim of this study was to investigate how the incubation parameters and microbial activity of the eggshell were affected by the disinfection of breeding quail eggs with water-based propolis extract in two different concentrations, 0.1% formalin, and distilled water prior to storage. A total of 480 hatching eggs of Coturnix coturnix (Japanese quail) were used and they were divided into a total of 5 groups (1 control and 4 separate treatment groups). Following the disinfection, the eggs were stored as 3 groups with different periods of storage, namely 7, 14 and 21 days before the incubation. In order to determine any microbiological activity, 100 eggs were used and aerobic-mesophilic bacteria counts were performed in a total of 5 groups on day 0, week 1, week 2 and week 3 for E. coli, yeast and mold, and Staphylococcus aureus. It was observed that the eggs stored for 3 weeks lost more weight in the pre-development period as compared to those stored for 1 and 2 weeks (P<0.01). Egg weight loss rates had a negative effect on hatching (P<0.01). Total amount of aerobic-mesophilic bacteria was low in the propolis group, medium in the 0.1% formalin group, and high in the water and control groups (P<0.05). Furthermore, it was found that the total amount of aerobic-mesophilic bacteria was higher in the shells of the eggs stored for 3 weeks as compared to those with a storage time of 1 and 2 weeks, which pointed to a statistically very significant relationship between the storage time and the total number of aerobic-mesophilic bacteria (P<0.01). On the other hand, yeast and mold growth varied according to treatment groups and storage time. The results suggest that propolis use does not have any negative effect on the incubation performance, to the contrary it keeps the microbial load in check during periods of storage and that it is safe to use in hatcheries.