Food commodities, including mycotoxins naturally produced from toxigenic fungi (pre- or post-harvest), are particularly vulnerable to contamination. The study intended to use unique bioactive composites loaded with antimicrobial constituents for food packaging. Three composite types are based on carboxymethyl cellulose/shellac (CMC/SH) and loaded with pomegranate extract (POE) with or without jojoba oil (JOE) at various concentrations. An enhancement was recorded for tensile strength and elongation at break and burst properties of the composites, where the results point out the amelioration of flexibility and elasticity with E9 (0.3/3 mg/mL of POE/JO). Moreover, E10 (0.3/1 of POE/JOE) content had higher phenolic and flavonoids, with significant antioxidants and the best antimicrobial and anti-mycotoxigenic activity. Six higher antimicrobial composites were chosen for corn seed coating applications in a simulated experiment of toxigenic fungal contamination, where the results recommend E10 as the best formula for packaging application. The E10 was characterized for emulsion stability, particle size, zeta potential, pH, PDI, and acidity that were recorded at 88.16 ± 2.87%, 54.81 nm, 38.74 mV, 6.34 ± 0.54, 31.12 ± 1.02, and 6.02 ± 0.34 mg/L, respectively. The in-silico study revealed that ellagic acid and hesperidin in POE extract, erucic and oleic acids in JOE, and shellac had the highest binding free energies against the vital enzymes involved in bactericidal/bacteriostatic effects and the aflatoxin bio synthetic mechanism.