In the present study, the effects of copper oxide nanoparticles (CuO NPs) on bioactive compounds, the ultrastructural modifications which can occur, and elemental content of wheat were investigated. Changes in the wheat plants grown in presence or absence of CuO NPs were estimated. The application of CuO NPs decreased the amounts of chlorophylls and carotenoids and increased the amounts of polyphenols and antioxidant capacity. Ultrastructural analysis showed that the plants treated with CuO NPs were negatively affected. Soil amending completely inhibited the accumulation of seventeen elements, while K, Br, Al, and Zn were accumulated and Cl, Na, Ba, and Sr content decreased in wheat samples, regardless of the type of NPs applied. The application of chemically obtained NPs induced the most significant changes, completely blocking the assimilation of Fe, Mo, As, Sb, and Sm, and favoring much higher accumulation of Br than biogenic NPs. The decrease in chlorophylls and carotenoids is correlated with increase in antioxidant capacity, and occurs with increase of Mo, Al, Mg, K, Zn, and Ca content. The behavior of total polyphenols is correlated with Br content, and antagonist to Al behavior. From the point of view of bioactive compounds, the most affected plants were those that grew in the presence of CuO-NP-cel, while from the point of view of elementary analysis, the most affected plants were those grown in the presence of CuO-NP. By corroborating the obtained results, it was found that the CuO NPs have a negative effect on wheat plants.