Propolis is a natural antimicrobial that can be used as a bioadditive in coatings to control fruit quality losses. The effect of two coatings was evaluated, a control (chitosan, 1%) and a treatment (chitosan, 1%; containing propolisethanolic extract, 5%), on the microbiological and physicochemical properties of papaya fruits. The chemical profile of the propolis revealed the presence of fatty acids and their esters, carbohydrates, diterpenic acids, and pentacyclic triterpenes. The fruits covered with the treatment demonstrated a reduced deterioration index and infection diameter of the fungus Colletotrichum gloeosporioides, as compared to the control papayas, postponing the appearance of damage by two days. Additionally, the treatment did not significantly affect the physicochemical properties of the papaya, as compared to the control. In conclusion, the coating formulated with propolis exhibited an in situ fungicidal and bactericidal effect without altering the physiological changes of the papaya fruit during storage.