The growing global population, along with evolving dietary trends and increasing concerns about health and the environment, underscores the urgent need to transform current food systems to minimize their environmental footprint and enhance global food security. This transformation has driven the development and demand for alternative food sources. In this context, alternative proteins emerge as promising options due to their production from plants, microorganisms, and insects, which potentially reduces the environmental impact of food production while supporting global food security. Nevertheless, the transition toward alternative proteins presents significant challenges related to the presence of antinutritional compounds, poor amino acid composition, lower digestibility, and undesirable organoleptic characteristics. Moreover, these new generations of alternative foods are highly processed, raising concerns about their nutritional adequacy compared to traditional products. In this context, fermentation technologies have emerged as promising tools to overcome these limitations. Traditional fermentation can degrade antinutritional factors, improve digestibility, and release bioactive compounds, allowing the production of new products with health-promoting properties. Beyond traditional fermentation, biomass fermentation to single-cell protein or microbial protein production represents a sustainable alternative, promoting a climate-friendly approach aligned with circular bioeconomy principles by upcycling various agro-industrial streams. Thus, this review discusses how microbial strategies (from traditional fermentation to cutting-edge microbial protein production) can enhance the nutritional properties of alternative protein-based foods. Emphasis is placed on the capacity of traditional fermentation to improve nutritional quality and bioactivity, mitigate undesirable sensory traits, and preserve or enhance micronutrient content. Additionally, integrating biomass fermentation and emerging precision fermentation positions microorganisms as valuable contributors to more nutritious and sustainable food systems.

The use of native microorganisms in craft beer and wine production represents a transformative approach that significantly enhances quality, sensorial complexity, and authenticity of the beverages. Integrating these microorganisms facilitates terroir expression, reduces dependence on commercial monocultures, and promotes sustainability by preserving native microbial biodiversity, which is vital to the identity of fermented craft beverages. This review analyzes the main roles of native yeasts, including Saccharomyces cerevisiae, Brettanomyces bruxellensis, Lachancea thermotolerans, Torulaspora delbrueckii, Pichia kudriavzevii , and Hanseniaspora spp., in shaping the biochemical and sensory profiles of craft beer and wine. It also provides a summary of the functions of lactic acid bacteria (LAB; Lactobacillus, Leuconostoc, Pediococcus, Oenococcus ) in malolactic fermentation and flavor development, as well as the effects of acetic acid bacteria (AAB; Acetobacter, Gluconobacter ) on oxidative complexity in select beverage styles. This work also highlights the use of mixed inoculation strategies and targeted strain selection to optimize fermentation kinetics, stress tolerance, and enzymatic activities, particularly those that enhance the liberation of aroma precursors. Additionally, challenges such as fermentation consistency, microbiological safety, and the need for standardized processes are also discussed. This framework provides essential insights to researchers and craft producers seeking innovation, product differentiation, and cultural preservation in the craft brewing and winemaking sectors, supporting regional economies and global biodiversity conservation through the scientifically grounded exploitation of native microorganisms.