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 …