Herein, CuO NPs were synthesized using an eco-friendly approach, characterized physicochemical and morphologically, and evaluated for their effects on agricultural seeds. To predict the response and identify the optimal synthesis conditions, a factorial design was employed to examine the effects of temperature and metal precursor concentration on CuO yield. Additionally, we propose a reaction mechanism to elucidate the formation of NPs and their interaction with the bioactive compounds in the extract. Finally, the CuO NPs obtained under the most favorable conditions were applied to Lactuca sativa (lettuce) and Solanum lycopersicum (tomato) seeds at varying concentrations, assessing their effects on physiological parameters related to seed germination and early seedling growth. Our findings may contribute to the advancement of more sustainable agricultural strategies by reducing reliance on synthetic fertilizers and promoting the valorization of plant waste in nanomaterial production.