The effects of high hydrostatic pressure (HHP) and heat treatments on antimicrobial protein stability and on the physico-chemical, microbiological, rheological and shelf-life properties of donkey milk were investigated. Although heat treatment at 75°C for 2 min resulted in 1.50 log CFU ml-1 microbial inactivation, losses in activities of lysozyme (58%) and lactoferrin (82%) were observed due to whey protein denaturation. By contrast, HHP application at 400 MPa caused lower enzyme activity losses (22 and 37% respectively) whilst maintaining a significant reduction of microbial load (1.80 log CFU ml-1). Color analyses showed that the lightness values of all samples decreased during storage. Higher flow consistency (viscosity) and lower flow behavior indexes were observed in heat-treated samples compared to untreated and HHP-treated ones, which can be explained by advanced protein denaturation during heat-treatment. The results suggest that HHP is a more suitable process than heat treatment for preservation of donkey milk within the conditions studied.