Copper (Cu) is widely used in agriculture as a pesticide and feed additive, but its intensive application has led to environmental accumulation in soils and plants, increasing dietary exposure in animals and humans. Copper-based nanoparticles (Cu-NPs) have emerged as a promising alternative to conventional forms due to their higher antimicrobial efficiency at lower doses, allowing reduced Cu inputs and potentially mitigating health risks. Nevertheless, their nanoscale dimensions confer greater reactivity, raising concerns about potential toxicity, particularly along the gut microbiota-immune axis, the primary interface for dietary Cu exposure. This review synthesizes findings from studies on the impacts of conventional Cu and Cu-NPs on intestinal health. Moderate Cu supplementation promotes livestock growth by enhancing gut morphology and supporting beneficial gut bacterial populations, whereas chronic or high-dose exposure is associated with intestinal toxicity. Similarly, Cu-NPs supplementation can improve livestock productivity, sometimes outperforming traditional Cu sources. However, comparative analyses reveal that Cu-NPs exhibit greater cytotoxicity than larger Cu forms at equivalent doses. Reported adverse effects linked to oral exposure to Cu-NPs include intestinal dysbiosis with reduced short-chain fatty acid production, impaired barrier integrity, and hepatorenal toxicity resulting from NP accumulation. This review highlights the dual nature of Cu and Cu-NPs, combining potential benefits with intestinal toxicity risks, and underscores the critical need for further research on their long-term impacts in agricultural animals and consumer safety. Further risk assessment is required to ensure that the agronomic benefits of Cu-NPs do not compromise host health and environmental sustainability.