Green (Penicillium digitatum) mold can severely endanger the citrus fruits production and quality. Targeting the protection of lemon fruits from green mold infestations with nanobiotechnology approach, the fenugreek seed mucilage (FM) was extracted and exploited for biosynthesis of selenium (SeNPs) nanoparticles; their nanocomposites (NCs) with chitosan (CT) was constructed and employed as antifungal materials and edible coating (ECs) to protect lemon fruits against green mold. The nanoparticles formation and conjugations were verified by infrared (FTIR) analysis and electron microscopy. The FM-synthesized SeNPs had particles average of 8.35 nm, were the NCs of them with CT had size mean of 49.33 nm and charged with +22.8 mV. The CT/FM/SeNPs composite exhibited superior antifungal actions toward P. digitatum isolates, up to 32.2 mm inhibition diameter and 12.5 mg/mL inhibitory concentration, which exceeded the actions of imazilil. The microscopic screening of exposed P. digitatum to NCs clarified their mycelial destructive action within 30 h. The coating of infected lemons with fabricated NCs led to complete elimination of green mold development after 10 days of coating, without any infestation remarks. The innovative fabrication of NCs from CT/FM/SeNPs is strongly suggested to protect citrus crops from green mold and preserve fruits quality.