Valorization of Plant-Derived Agri-Food Byproducts in Functional Beverages: Matrix Engineering, Microbiota Modulation, and Translational Challenges

Despite the growing incorporation of plant-derived agri-food byproducts into beverage formulations, translating their bioactive potential into consistent physiological outcomes remains challenging. Functional performance is determined not only by the composition of bioactive ingredients but also by beverage matrix engineering, processing conditions, physicochemical stability, gastrointestinal bioaccessibility, and regulatory readiness. This review critically examines the valorization of plant-derived agri-food byproducts in functional beverage applications, with particular emphasis on matrix engineering strategies that enhance the stability, dispersibility, sensory quality, and delivery of bioactive compounds. The review further discusses how beverage matrix composition influences pH stability, phase behavior, flavor profile, and gastrointestinal interactions, thereby shaping biological performance. In addition, current evidence regarding the capacity of bioactive ingredients derived from plant-based byproducts to modulate the gut microbiota is evaluated from a mechanistic perspective. Translational challenges associated with industrial implementation, including formulation feasibility, physicochemical stability during storage, safety assessment, scalability, regulatory approval, and consumer acceptance, are also critically discussed. Available evidence indicates that many reported health benefits originate from controlled experimental models that only partially represent commercial beverage systems. Therefore, future research should prioritize integrated formulation strategies that combine sustainable byproduct valorization with beverage matrix optimization, mechanistic validation, and translational evaluation to bridge the gap between experimental evidence and commercially relevant functional beverage applications.