The aim of the present research was to evaluate differences in chemical properties and physical structure of yoghurt produced with milk from different species (sheep, cow, and goat). For each trial, whole raw sheep (S), cow (C), and goat (G) milk were used to manufacture 4L of yoghurts (Y) from each species (SY, CY, and GY, respectively). The SY demonstrated the greatest (P<0.05) values of total solids, protein, and lipid contents, reflecting on greater (P<0.05) firmness, apparent viscosity and water-holding capacity, and lower (P<0.05) syneresis index than CY and GY. Consequently, SY exhibited a more compact microstructure and homogeneous matrix with fewer pores. Furthermore, CY and GY microstructure contained a greater number of pores, which exhibited greater size heterogeneity than SY. Therefore, based on the evaluated physicochemical and microstructural properties of yoghurt, SY demonstrated the most desirable parameter values for dairy industry representing an alternative substitution for cow’s milk yogurt.