The stability of the physicochemical characteristics of yoghurts during refrigerated storage is important for industry and the consumer. In this study we produced plain yoghurts with the addition of health-promoting whey protein concentrate (WPC), using two different starter cultures based on Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. Physicochemical changes (acidity, nutritional value, water activity, water-holding capacity, texture, and colour, including whitening and yellowing indices) as well as sensory changes occurring during 28-day refrigerated storage were determined. Starter cultures were found to significantly (p ≤ 0.05 and p ≤ 0.01) influence the water-holding capacity, firmness, consistency, cohesive strength and colour parameters of the curd. Use of whey protein concentrate affected both the physicochemical and sensory quality of the yoghurts. The additive had a significant effect on potential acidity, inhibiting the increase in lactic acid in the yoghurts during storage, and also reduced syneresis. However, it decreased the lightness of curd and negatively affected its sensory characteristics, primarily flavour. Moreover, nearly all parameters changed significantly with the passage of storage time (in most cases negatively). The exceptions were total protein and fat content. The changes, however, were not severe and remained at a level acceptable to tasters. Addition of 1% or 2% whey protein to yoghurt may be a good solution that can be routinely applied in the dairy industry to offer consumers a new functional product. A comprehensive assessment of the physicochemical and sensory changes occurring during refrigerated storage of yoghurts manufactured with the addition of WPC and using different cultures is crucial for modelling such a product.