The aim of the research was to assess changes in the bioactive status of organic yoghurts produced in the spring/summer season from Simmental cows’ bulk milk during 28-day refrigerated storage, including whey proteins, lipophilic vitamins, and free fatty acids, and to interpret these changes not only in terms of compositional stability but also regarding their nutritional significance, as evaluated using the IYQ (Index of Yoghurt Quality) for vitamins. Raw milk was found to be a significantly richer source of biologically active compounds compared with milk subjected to heat treatment. During the 28-day refrigerated storage of the yoghurts, unfavourable alterations were observed in the levels of selected bioactive components belonging to both the protein and lipid fractions. A reduction in the concentration of the analyzed proteins and vitamins was observed, ranging from 2% for vitamin D3 to 38% for lactoferrin, while the content of free fatty acids increased, from 8% for monounsaturated free fatty acids (MUFFAs) to 39% for short-chain free fatty acids (SCFFAs). The most pronounced changes were observed in lactoferrin content (p ≤ 0.01), whereas vitamin D3 exhibited the highest stability throughout the storage period. The stability of vitamin D3 was further confirmed using the Index of Yoghurt Quality (IYQ). Despite the significant changes observed in the bioactive profile, the yoghurts retained high sensory quality throughout the entire storage period. This indicates that alterations in bioactive status did not compromise the sensory quality of the product, even after 28 days of storage (i.e., at the end of the shelf life). The obtained results indicate the feasibility of developing organic milk processing directly at the farm level while preserving the nutritional value of the products. The possibility of processing organic milk not only into cheese but also into fermented dairy beverages, particularly yoghurts, is of key importance for farmers aiming to diversify production, increase added value, and improve the economic sustainability of small-scale organic farms.