Traditional fermented foods and beverages, typical of a given region, represent a source of biodiversity for the development of innovative, sustainable and health-oriented foods. Another source of biodiversity is various spices and herbs, which are typical of the diet of different countries. The aim of this work is to make a critical analysis of fermented foods and beverages typical of Bulgaria and France, as well as spices and herbs as a source of biodiversity for the development of innovative fermented and biopreserved foods. The paper focuses on methodological approaches for the isolation, identification, genetic characterization, and functional screening of lactic acid bacteria and yeasts from artisanal fermented matrices, highlighting process-relevant traits such as antimicrobial activity, probiotic potential, fermentation performance, and technological stability. In parallel, the review critically evaluates process-oriented methodologies for the selection, extraction, physicochemical characterization, and antimicrobial assessment of plant-derived bioactive compounds, including extracts and essential oils obtained from traditional herbs and spices. Finally, the compatibility between plant extracts and microbial strains used for the fermentation of foods and beverages is discussed.