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 for delaying microbial growth and maintaining mushroom quality. This study examined the effects of a nano-chitosan (NC) and 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 prepared using the enzyme Alcalase. Five edible films containing NC, NC-AV, and varying concentrations of TPH (0%, 0.5%, 1%, 1.5%) were produced. The relationship between the concentration of TPH and the resulting physicochemical properties was investigated. The shelf lives of coated mushrooms were evaluated during 16 days of refrigerated storage (4 ± 1 °C). Results showed that TPH had high levels of protein (90.16%), hydrophobic amino acids (31.78%), and aromatic amino acids (11.74%). The produced films exhibited significant antioxidant and antimicrobial activities, with improvements observed at higher concentrations of TPH (P < 0.05). The interaction between the protein hydrolyzate film and the mushroom’s natural proteins may enhance nutrient retention and stability. 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 reduction of microbial spoilage (P < 0.05). Sensory evaluation indicated that the sample containing 1.5% TPH had the highest overall acceptance. The NC-AV composite coating containing TPH effectively extended the shelf life of button mushrooms by approximately 8 days.