Copper has been used as an antimicrobial agent for over a century and is now being added to commercial fungicides. Nanomaterials have attracted much attention due to the special properties they have over their bulk form. We studied nanostructured copper (Cu-NPs), investigating the potential for improved antifungal properties derived from its special properties and studied any effect that the oxidation of copper (CuO-NPs) may have. We conducted this research against Colletotrichum gloeoesporioides, a devastating pathogen to plants/crops worldwide. Research on the effects of copper on this fungus are limited. Our studies showed that nanoforms of copper had significant antifungal activities, with Cu-NPs offering the most sustainable efficacy and was more effective than its oxidative form (CuO-NPs). Scanning Electron Microscopy (SEM) images of the treated pathogen show that the hyphae had a swollen appearance, lost their filamentous structure, and the mycelia had a powder-like structure, indicating the probable destruction of the hyphal tubular cell wall. X-ray Difractogram (XRD) outputs showed substantial changes in the physical characteristics of the Cu-NPs after interaction with the fungus. This is the first report to demonstrate chemo-physical changes in the metal compounds, opening new insights for further studies on the mechanism of copper’s antifungal properties.