Sea buckthorn fruit is abundant with essential nutrients and bioactive substances, yet it remains less sought after. Therefore, it is valuable to explore new ways of sea buckthorn fruit processing, which can boost consumer acceptance of sea buckthorn fruit and also lead to formulation of new functional foods. In the presented review, we summarize studies focused on development of foods utilizing sea buckthorn fruit or its components and bacterial food cultures. Firstly, we discuss the impact of malolactic fermentation on content and profile of organic acids and polyphenols of sea buckthorn fruit juice. During this process, changes in antioxidant and sensory properties are considerable. Secondly, we address the role of sea buckthorn fruit and its components in formulating novel probiotic dairy and non-dairy products. In this regard, a synergic effect of prebiotic material and probiotic bacteria against pathogens is distinguished. Overall, the potential of sea buckthorn fruit as a botanical ingredient for application in novel foods is highlighted.