Button mushroom (Agaricus bisporus) is a widely consumed edible mushroom, but its quality deteriorates rapidly after harvest. Therefore, the use of edible coatings with natural preservative compounds is essential to delay and reduce microbial growth and maintain mushroom quality. This study examined the effects of a nano-chitosan (NC)-aloe vera (AV) edible coating combined with tomato seed protein hydrolyzate (TPH) as a natural preservative on the chemical, microbial, and organoleptic properties of button mushrooms. TPH was initially prepared using the enzyme Alcalase. Five edible films containing NC, NC-AV, and varying concentrations of TPH (0%, 0.5%, 1%, 1.5%) were then produced. The shelf lives of coated mushrooms were evaluated during 16 days of refrigerated storage (4 ± 1°C). Results showed that the TPH had high levels of protein (90.16%), hydrophobic amino acids (31.78%), and aromatic amino acids (11.74%). The produced films exhibited high antioxidant and antimicrobial activities, with improved results observed at increased concentrations of TPH. Compared to uncoated mushrooms, the nanocomposite coatings significantly reduced physicochemical changes, quality degradation, and microbial spoilage. Increased concentrations of TPH further enhanced browning inhibition, free radical scavenging, and microbial spoilage reduction (p < 0.05). Sensory evaluation indicated that the sample containing 1.5% TPH had the highest overall acceptance. The use of a NC-AV composite coating containing TPH can be an effective method for extending the shelf life of white button mushrooms.