The objective of the research was to determine changes resulting from the activity of bacteria (Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus) in model samples of yoghurt during their cooling storage. The profiles were compared of volatile compounds produced in the milk that was fermented by a yoghurt culture and in the milk that was not fermented, but contained those bacteria. The results obtained showed an intensive increase in the concentration of all the volatile compounds in the fermented and non-fermented milk samples in the fourth week of storage. The fermentation process was found to be highly vital for the production of such compounds as: butyric acid, isovaleric acid, capronic acid, and acetoin, whereas the compounds: 2-heptanon, 2-pentanon, and 2-butanon occurred mainly owing to the auto-oxidative transformations of milk components during the storage. The occurrence of alcohols proved the enzymatic activity of bacteria subject to the pH level of the environment. It can be concluded that measuring the levels of the compounds contained, such as acetoin, butyric acid, or propionic acid, can support the planning and control of the fermentation process duration period and of the storage time of fermented milk products, as can guarantee their constant and required sensory quality.