Given the risks associated with synthetic fungicides, it is crucial to explore safe and sustainable alternatives. One potential solution is using bioactive natural products (BNPs). However, BNPs face challenges like lability, solubility, and lack of specificity. These issues can be addressed through nanoencapsulation. This study focuses on the evaluation of novel chitosan oligomers–hydroxyapatite–carbon nitride (COS–HAp–g-C3N4) nanocarriers (NCs) for encapsulating BNPs, specifically an extract from Uncaria tomentosa bark. The NCs were characterized by transmission electron microscopy, energy-dispersive X-ray spectroscopy, and infrared spectroscopy. The NCs were monodisperse, with a mean diameter of 250 nm, and showed an encapsulation efficiency of 82%. The suitability of the loaded NCs (COS–HAp–g-C3N4–BNP, in a 2:1:0.5:1 weight ratio) for postharvest fruit protection was investigated in vitro and ex situ at a laboratory scale. Results regarding their efficacy against Botrytis cinerea on strawberries, Colletotrichum gloeosporioides on mangoes, Penicillium expansum on apples, Monilinia laxa on peaches, and Sclerotinia sclerotiorum on kiwifruit are presented. Minimum inhibitory concentrations of 250, 375, 375, 250, and 187.5 μg·mL−1 were found in vitro, respectively, while higher doses (500, 750, 750, 250, and 375 μg·mL−1, respectively) were needed to achieve effective control in postharvest tests on artificially inoculated fruit. These findings suggest that NCs containing extracts from U. tomentosa bark show promise as biorational agents and as alternatives to conventional fungicides for managing postharvest phytopathogens
