Ten percent of the world’s total edible eggs come from Japanese quail. The popularity of quail eggs is attributed to their high yolk content and hypoallergenic properties. This study aimed to analyze the physical characteristics and selected biochemical parameters of Japanese quail eggs based on shell color (dotted - D group, spotted - S group, and hazy - H group). The heaviest and most elongated eggs were found in the group H. The yolk index was significantly higher in dotted eggs, which also exhibited the highest lysozyme content and activity. The thickest shell (p≤0.05) with the lowest elasticity was observed in hazy eggs. However, no differences were found between eggshell colors concerning their breaking strength. The highest Ca content in the shell was found in the spotted group (S), while hazy eggs exhibited the lowest (p≤0.05) Ca and Mg content, despite having the thickest shells. Hazy eggs were also characterized by the highest crude protein content and the smallest proportion of crude fat and ash. The dotted eggs had the highest (p≤0.05) proportions of C16:1 and C18:2 fatty acids and a higher PUFA content (p≤0.05). Nutritionally, the dotted eggs performed best in terms of fatty acid profile and were also characterized by higher Mg, Ca, Cu, Mn, K, and Na content compared to the other groups. In summary, dotted eggs may be more appealing to consumers due to their advantageous physical and biochemical characteristics.