Background Nutritional interventions with natural antioxidants can provide a pragmatic solution for modifying hens’ performance and maintaining oxidative stability of eggs during storage. Quercetin is the most abundant flavonoids with potent antioxidant and immune stimulant activities. The concept of incorporating of quercetin, as potent antioxidant and immunostimulant, into effective nano-carriers (QNPs) has promoted their bioavailability and stability thus, their effectiveness for the first time were assessed on laying hens’ performance and immunity, eggs quality during storage. Four hundred 12-weeks-old Hy-line brown laying hens were distributed to four experimental groups: control group fed basal diets, and other 3 groups fed basal diets fortified with 100, 200 and 300 mg/kg QNPs for 60 weeks. Results Laying performance and quality of laid eggs were improved as expressed by elevated laying rate, egg mass %, eggs weight and yolk weight in QNPs200 and 300. Fortification of QNPs300 remarkably decreased layers serum total cholesterol concurrently with decreased egg yolk saturated fatty acids and cholesterol while increased polyunsaturated fatty acids. Over- 45 days storage period, QNPs enhanced phospholipids, total phenolics and flavonoids, total antioxidant activity (T-AOC) simultaneous with decreased MDA content in eggs. Furthermore, enhanced immune response was detected in both in serum and intestine of QNPs fed hens as reflected by higher lysozymes activity, IgM, IgG and phagocytic index and demotion of NO together with AvBD 6–12, IL-10, IgM and ATg 5-7-12 upregulation and downregulation of IL-1β and TNF-α especially at QNPs200 and 300. Intestinal redox balance was modified via decreasing H2O2 and MDA simultaneous with upregulation of catalase, SOD, GSH-Px, HO-1 and NQO1 in groups fed higher doses of QNPs.