Abstract Background Citrus production and trading are seriously affected by fungal decays worldwide; the green mold infection by Penicillium digitatum could be the most disastrous. The substitutions of chemical and synthetic fungicides with effectual natural alternatives are global demands; plant extract from pomegranates peels (PPE), biosynthesized selenium nanoparticles with PPE (PPE/SeNPs) and chitosan nanoparticles (NCT) were suggested as efficacious fungicidal agents/nanocomposites to control P. digitatum strains. Method PPE from Punica granatum was extracted and employed directly for synthesizing SeNPs, whereas NCT was produced using ionic gelation method of chitosan extracted from white prawn (Fenneropenaeus indicus) shells. The physiochemical, biochemical and structural characterization of generated molecules were conducted using infra-red spectroscopy, particles’ size (Ps) and charge assessment and electron microscopes imaging. Antifungal potentialities were investigated in vitro and in infected fruits with P. digitatum by applying NCT nanocomposites-based edible coating. Results The synthesis of PPE-synthesized SeNPs and NCT was successfully achieved, the molecular bonding in synthesized agents/composites were proved with infrared spectroscopy to have both biochemical and physical interactions. The nanoparticles had 82.72, 9.41 and 85.17 nm mean diameters for NCT, PPE/SeNPs and NCT/PPE/SeNPs nanocomposites, respectively. The nanoparticles had homogenous spherical shapes and good distribution attributes. The entire agents/nanocomposites exhibited potent fungicidal potentialities toward P. digitatum isolates; NCT/PPE/SeNPs nanocomposite was the most forceful and significantly exceeded the fungicidal action of standard fungicide. The direct treatment of fungal mycelia with NCT/PPE/SeNPs nanocomposite led to remarkable lysis and deformations of P. digitatum hyphae within 12 h of treatment. The coating of infected orange with NCT-based edible coatings reduced the green mold infection signs by 91.7, 95.4 and 100%, for NCT, NCT/PPE and NCT/PPE/SeNPs based coating solutions, respectively. Conclusions NCT, PPE-synthesized SeNPs, and their innovative nanocomposites NCT/PPE/SeNPs are convincingly recommended for formulating effectual antifungal and edible coatings to eliminate postharvest fungal pathogen, both with protection from their invasion or with destructing their existing infections. Graphical Abstract