The cheese rind is the natural food packaging of cheese and is subject to a wide range of external factors that compromise the appearance of the cheese, including color defects caused by spoilage microorganisms. First, eight films based on whey protein isolate (WPI) coatings were studied, of which IS3CA (WPI 5% + sorbitol 3% + citric acid 3%) was selected for presenting better properties. From the IS3CA film, novel films containing melanin M1 (74 µg/mL) and M2 (500 µg/mL) were developed and applied to cheese under proof-of-concept and industrial conditions. After 40 days of maturation, M2 presented the lowest microorganism count for all the microbial parameters analyzed. The cheese with M2 showed the lowest lightness, which indicates that it is the darkest cheese due to the melanin concentration. It was found that the mechanical and colorimetric properties are the ones that contribute the most to the distinction of the M2 film in cheese from the others. Using FTIR-ATR, it was possible to distinguish the rinds of M2 cheeses because they contained the highest concentrations of melanin. Thus, this study shows that the film with M2 showed the best mechanical, chemical and antimicrobial properties for application in cheese.