Food industry has mostly focused on natural preservatives due to the undesirable effects of chemical additives on the human health. Among milk proteins, lactoferrin and lysozyme are the best-known for their antimicrobial. In this study, lactoferrin and lysozyme were extracted from donkey milk and applied on the yoghurt surface by spraying. The obtained yoghurt samples enriched with antimicrobial proteins were compared with the control sample produced without the addition of any preservatives as well as the samples treated with natamycin, a commercial preservative used in dairy products. Thereby physicochemical, microbiological and textural properties of the samples were investigated during the 30 days of storage. Yoghurt samples treated with antimicrobial agents had lower microbial load than control samples, which indicated that the donkey milk lactoferrin and lysozyme inhibit microbial activity in yoghurts. However, the addition of the mentioned preservatives did not change the gross composition and the textural properties of the yoghurt samples. Most importantly, the incorporation of lactoferrin or lysozyme did not adversely affect the sensory properties of yoghurt samples, but achieved higher appreciation points than the control sample on the 30th day of storage. In brief, lactoferrin and lysozyme extracted from donkey milk could be used to control the undesirable microbial growth, hence extending the shelf life of yoghurt.