The fruit infection by fungi reduces the quantity and quality of food for human consumption and causes economic damage. Thus, this study aimed to address the effects of nanocapsules (NCs) based on chitosan and carboxymethylcellulose containing eugenol in protecting nectarines against Monilinia fructicola, a brown rot agent, a worldwide important disease. NCs were prepared by Layer-by-Layer self-assembly starting from an anionic template and deposition with up to two polymeric layers. The sizes ranged from 158 nm (nanoemulsion) to 398 nm (two polymeric layers). In vitro release showed an initial burst followed by a gradual release. In addition to showing a good adherence to nectarine surface, the NCs coated with chitosan proved to be the best formulation for the control of brown rot in the antifungal test. Therefore, this study demonstrated that chitosan NCs containing eugenol could be an alternative to preserve fruit for longer periods in the post-harvest.