The use of copper hydroxide nanopesticide can pose exposure risks to aquatic organisms. In this study, the toxicity of a copper hydroxide nanopesticide, compared to conventional copper sulfate at environmentally relevant doses, was evaluated using metabolomics and bioenergetic assays in embryonic zebrafish. At a copper concentration of 100 μg/L, the nanopesticide caused higher mortality and deformity compared to copper ions alone; despite higher copper accumulation, increased metallothionein and elevated ATP-binding cassette (ABC) transporter activity in zebrafish exposed to copper ions were observed. Both nanopesticide and copper ions reduced the abundance of metabolites of glycolysis and induced energetic stress in zebrafish. The nanopesticide also increased concentrations of several organic acids involved in the tricarboxylic acid (TCA) cycle and elevated the activity of isocitrate dehydrogenase and α-ketoglutarate dehydrogenase, suggesting enhanced TCA cycle activity. Nanopesticide exposure depleted both glutamate and glutamine parallel to the upregulation of the TCA cycle. In addition, zebrafish exposed to the nanopesticide appeared to shift metabolism toward amino acid catabolism and lipid accumulation based upon altered expression profiles of glutaminase, glutamate dehydrogenase, fatty acid synthase, and acetyl-CoA carboxylase. Lastly, the ability of the ions to increase oxidative phosphorylation to alleviate energetic stress was reduced in the case of the nanopesticide. We hypothesize that, unlike copper ions alone, the nanopesticide induces higher toxicity to zebrafish because of increased protein catabolism. This study provides a comprehensive understanding of the risks of copper hydroxide nanopesticide exposure in relation to metabolic activity and mitochondrial function.