Phytogenic feed additives in poultry demonstrate phenotypic improvements and potentially possess humoral significance for organ systems involved in egg production, digestion, and excretion, warranting further investigation into their mechanisms of action. These additives contain a wide array of active ingredients with antimicrobial, immunomodulatory, and antioxidant properties, positioning them as a promising alternative to in-feed antibiotics for enhancing poultry performance and welfare. This study investigates how a phytogenic feed supplement based mainly on essential oils of thyme and star anise with quillaja bark influences reproductive and nutrient-utilizing tissues and nutrient bioavailability in laying hens. A four-week trial with Lohmann Brown hens aged 68 weeks was conducted using diets with or without 150 mg/kg phytogenic supplement to assess performance (n = 96), egg quality (n = 96), nutrient digestibility (n = 24), and gene expression in pancreas, kidney, uterus, and follicles (n = 20 per tissue). Supplemented laying hens showed a significant increase of 3.84 % (p = 0.001) in the apparent ileal digestibility of crude protein and trends for improved egg weights (p = 0.053) and feed-to-egg mass ratio (p = 0.079) compared to control-fed hens. Complementary RNA sequencing analyses revealed differentially expressed genes (adjusted p-value < 0.05) with antimicrobial properties (pancreas, follicles) and an influence on bio-mineralization processes (uterus). Results suggest improved cleavage of carbohydrates, peptides, and lipids in the follicle, indicating improved nutrient utilisation for the developing embryo. Consequently, the implementation of phytogenics improves nutrient digestibility of laying hens and promotes resource reallocation in the hen towards the immune system and nutrient availability in eggs, potentially benefiting both in-ovo development and egg quality. A targeted phytogenic feed supplement can enhance the expression of antibacterial proteins involved in innate immune responses.