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Abstract Engineered nanomaterials have unique properties compared to their bulk counterparts. Copper oxide nanoparticles (CuO NPs) are one example of nanomaterials used in a wide range of consumer products due to their conductivity and biocidal properties. While CuO NPs can induce toxicity in various organisms, their interactions with different organisms and how they affect cellular homeostasis is yet to be fully understood. In this work, the toxicity of CuO NPs was evaluated in different human cell lines (colorectal carcinoma, cervical cancer, embryonic kidney, and lung fibroblast), showing a dose-dependent toxicity. An untargeted lipidomics approach using liquid chromatography-quadrupole time of flight mass spectrometry was employed in a human colon carcinoma cell line to investigate the impact of CuO NP exposure at the cellular level. A 24 h CuO NP exposure at 2.5 and 5 μg mL−1 resulted in upregulation of different metabolites: triacylglycerols, phosphatidylcholines, and ceramides accumulated. The most profound increase in a dose-dependent manner was observed in ceramides, specifically in C18:0, C18:1, and C22:0 species, with up to ∼10 fold accumulations. Further experiments suggested that activation of autophagy and oxidative stress could be responsible for the toxicity observed in these cell lines. Increases in the level of glutathione oxide (∼7 fold) also supported the activation of oxidative stress upon CuO NP treatment. Based on the changes in different metabolites induced by CuO NP exposure and previous studies from our laboratory, we propose that autophagy and oxidative stress could play a role in CuO NP-induced toxicity.