The stability of the physico-chemical and sensory characteristics of yoghurts during refrigerated storage is important for industry and the consumer. The aim of the study was to evaluate the nutritional value, microbiological quality, sensory properties, and structure of natural probiotic yoghurts made with the addition of sea buckthorn fruit mousse during refrigerated storage. In this study, we produced natural, probiotic organic yoghurts with the addition of superfoods, i.e., sea buckthorn (Hippophae rhamnoides L.) fruit mousse, using ABT-1 probiotic yoghurt starter culture based on Lactobacillus acidophilus LA-5, Bifidobacterium lactis BB-12, and Streptococcus thermophilus. Physico-chemical (acidity, nutritional value, and structure) as well as microbiological and sensory changes occurring during 21-day refrigerated storage were determined. The yoghurts were characterized by high sanitary and hygienic quality during the whole refrigerated storage. Fourier-Transform Infrared (FTIR) spectra were also used in the analyses of the obtained yoghurt samples. The applied yoghurt additive was visible at the spectral level as an increase in the intensity of the characteristic bands for vibrations related to protein, fat, and polysaccharide structures. Sea buckthorn can be used as a modern and unconventional addition to yoghurts with health-promoting properties. Micrographic studies have shown that the addition of sea buckthorn mousse significantly changes the microstructure of the yoghurt. The structure of sea buckthorn to yoghurt seems to be more susceptible to the influence of damaging factors, which is also confirmed by the FTIR test conducted during the storage