In this study, chitosan nanoparticles are used to encapsulate didymin and flavonoids separately using ionic gelation with phytic acid as a cross-linker. Their structural, antioxidant, and antifungal properties were evaluated. Flavonoid (Fs) was extracted from orange peels, while didymin (Did) was qualified in the pure extract using ultra-performance liquid chromatography (UPLC). UV-vis spectroscopy and FTIR confirmed the interaction of the obtained nanoparticles, which aligned with Surflex-dock findings. These nanoparticles showed a more compact structure and excellent thermal stability. The encapsulation efficiency (EE%) of Did-Cn and Fs-Cn nanoparticles was 55.33 ± 3.51 and 47.40 ± 0.56 %, respectively. The antioxidant assay showed that these nanoparticles highly reduced FRAP, DPPH, and ABTS radicals. The growth inhibition of Penicillium expansum was 37.39 ± 1.07 %, that of Aspergillus westerdijkiae was 44.26 ± 1.05 %, and that of Alternaria alternata was completely inhibited, which fits with clicks of the confocal microscope. These results suggest that food packaging or coatings could incorporate these nanoparticles to prevent fungal spoilage, thereby improving food safety. Meanwhile, using such nanoparticles offers a natural, safe, and effective solution for the pharmaceuticals and/or food industries to extend the freshness and shelf life of fruits and perishable items, reducing reliance on synthetic preservatives.