This systematic narrative review aims to catalogue bioactive compounds that are formed during the fermentation process and identified as contributors to positive health outcomes in human clinical studies where fermented foods were used as dietary interventions. Under “The European Cooperation in Science and Technology” (COST) Action CA20128 – “Promoting Innovation of Fermented Foods" PIMENTO framework, a systematic literature search was conducted across PubMed, Scopus, and the Cochrane Library. The search initially identified 2,411 studies, of which 50 met the predefined inclusion criteria. In all included studies, fermented foods were used as nutritional interventions, and the bioactive compounds they contained were either hypothesised or directly analysed in relation to statistically significant health effects observed in humans. Findings were summarised in “Population, Intervention, Comparator, Outcome” (PICO)-structured tables and classified by health domain. The reported effects were grouped under the following categories: cardiovascular health, lipid metabolism, glucose regulation, immune modulation, neuroprotection, liver function, and other health outcomes. Across the included studies, a total of 31 bioactive compounds and/or compound groups were identified in fermented foods, including bioactive peptides, polyphenols (epicatechin, genistein), γ-aminobutyric acid (GABA), acetic acid, curcumin, and arabinoxylans. The mechanisms of action associated with these compounds were explored in the non-systematic section of the review, supported by findings from in vitro, animal and human studies. By linking individual bioactive compounds derived from fermented foods to clinical outcomes and underlying mechanisms, this review provides a comprehensive and functional resource for nutritional science, fermented food innovation, and public health applications.