Milk-derived extracellular vesicles (MEVs) modulate metabolic and immune processes. Donkey milk, given its compositional similarity to human milk and documented bioactivities-including antioxidant, anti-inflammatory, and anti-cancer properties-represents a promising source for therapeutically relevant EVs. However, standardized protocols for efficient donkey milk EVs isolation remain limited. This study compared two isolation methods for donkey milk EVs: conventional ultracentrifugation (UC) and the ultrafast isolation system EXODUS (DUS). We systematically evaluated MEV morphology, particle size distribution, and marker protein expression profiles. Subsequently, we performed comprehensive proteomic characterization using 4D label-free quantitative proteomics. Both isolation methods yielded MEVs with characteristic spherical or elliptical membrane structures. UC-isolated MEVs showed significantly higher particle concentrations compared to DUS-isolated vesicles; however, UC extraction introduced polymer precipitates and protein particle contaminants. Proteomic analysis identified 1220 proteins across both isolation methods. Gene Ontology annotation revealed distinct protein enrichment patterns: DUS-isolated MEVs showed enhanced representation of proteins associated with extracellular regions, extracellular matrix, and extracellular exosomes, while UC-isolated MEVs were enriched in proteins related to GTP binding, GTPase activity, and early endosome functions. These findings suggest that DUS extraction preserves greater MEV structural integrity. KEGG pathway enrichment analysis demonstrated that differentially expressed proteins from each extraction method exhibit distinct biological functionalities. These findings reveal that DUS extraction preserves superior structural integrity and functional capacity, while UC provides higher yield at the cost of increased contamination. This systematic framework enables researchers to align extraction strategy with specific applications, advancing both fundamental investigation of donkey milk bioactivities and industrial-scale production of therapeutically relevant EVs.