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Possible impacts of nanofertilizer-mediated agriculture were assessed by studying the effects of copper and copper oxide nanoparticles (CuNP and CuO NP) on barley (Hordeum vulgare L.) seedlings. Liquid chromatography coupled to mass spectrometry and gas chromatography coupled to mass spectrometry revealed qualitative and quantitative changes in many phytochemicals. CuNP and CuO NP caused depletion of several phenolic acids and flavonoids, which may reduce the antioxidant potential of foods derived from barley. An additional effect was noted as a deficiency in some bioactive compounds such as the volatile organic compounds. In addition, an imbalance in essential minerals may have impacts on biochemical and physiological functions in the human body. Alteration of nutritional quality, added to the accumulation of toxic cupric ions and hazards associated with possible induction of oxidative stress raise concerns about use of Cu and CuO based nanofertilizers in agriculture without more rigorous risk-assessment.