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Banana (Musa paradisiaca) is among Ecuador’s most important export commodities, globally recognized for its high nutritional value. To extend shelf life and reduce physiological and microbiological deterioration, bananas are typically harvested at the green stage and stored under controlled conditions using plastic packaging. This study evaluated the combined effect of an antifungal coating—formulated with whey, cassava starch, glycerol, agar, and 600 ppm cinnamon essential oil—and polyethylene bags of different densities (LDPE and HDPE) over a 28-day storage period. Eight treatments were tested, including various coating–packaging combinations from three producers, as well as plastic-only and unpackaged controls. Physicochemical results showed that the coating combined with LDPE significantly reduced weight loss, peel and length shrinkage, and firmness decline. Color retention (ΔL*, Δa*, Δb*) and soluble solids were better preserved in coated samples, especially T05 and T06. Sensory evaluation with 18 panelists revealed the highest acceptance scores for coated and packaged fruit. Microbiological analyses confirmed that coated bananas had the lowest counts of mesophilic aerobes and yeasts and molds, while total coliforms remained below detection limits in all treatments. These results highlight the effectiveness of integrating antifungal coatings with polyethylene packaging to enhance banana quality during postharvest storage.