This study evaluated the effects of natural pigments, such as paprika extract and marigold flower extract, on performance, egg quality, carotenoid content in the yolk, and shelf life of Japanese quail eggs. The experiment included 160 birds, divided into 4 treatment groups, as follows: 0.8% paprika extract, 0.8% marigold flower extract, 0.8% paprika/marigold (P/M) mixture, and a control group. The experiment lasted 84 days. The inclusion of paprika, marigold, or their combination did not affect performance parameters, except for feed conversion, which was significantly poorer in the supplemented groups compared to the control. An improvement in yolk color was observed, particularly in the marigold group, which showed higher concentrations of β-carotene (40 g/kg). Yolk color intensity, measured using the L*, a*, and b* scales, was enhanced in all supplemented groups. During storage, yolk weight increased after 5.72 days, while albumen weight showed a significant reduction starting at 4.30 days, with a more pronounced decrease after 6.6 days. Albumen diameter expanded after 15.7 days of storage, and the Haugh unit was significantly affected from the 17th day onward. Yolk percentage decreased after 4.06 days, while albumen and eggshell percentages decreased after 4.10 and 3.41 days, respectively. These results suggest that paprika and marigold extracts are effective in improving yolk color and maintaining egg quality without compromising performance. However, a poorer feed conversion by mass was observed in the groups fed with the paprika, marigold, and the (P/M) mixture, compared to the control group. These natural pigments also positively impacted egg quality, particularly in terms of color intensity and internal parameters, and helped maintain egg quality during storage, meeting consumer expectations for high-quality products. Future studies should focus on evaluating the antioxidant effects of these pigments in eggs, as this could provide a deeper understanding of their potential benefits, both in terms of nutritional quality and shelf-life enhancement.