The impact of cooling temperatures on gel characteristics of set-type yoghurts was investigated through 28 days of storage. Yoghurt samples were cooled at four different temperatures (−10 °C, −5 °C, 0 °C, 4 °C) after incubation until the central temperature of yoghurt cups reached 4 °C. Cooling temperature and storage period were determined as significant factors affecting the yoghurt gel characteristics (p < 0.05). Yoghurts cooled at 0 °C clearly differed from the other yoghurts in terms of gel firmness and consistency. Confocal images of yoghurts cooled at 0 °C showed more homogeneous protein matrix than the other samples. Microbial counts and the acidity of the yoghurt samples increased with storage period. Textural parameters, water holding capacity and susceptibility to syneresis increased until 14th day of storage and then decreased. Sensory analysis of yoghurt samples confirmed the results obtained by microbiological and textural measurements.