The convergence of probiotic, synbiotic, and enzyme-assisted fermentation technologies represents a paradigm shift in modern agri-food systems, offering transformative approaches to nutritional enhancement, functional food development, and sustainable processing. This review examines the emerging trends and technological innovations at the intersection of these three complementary fermentation strategies, with particular emphasis on their applications in agricultural value addition and sustainable food production. The scope encompasses the characterization of probiotic microorganisms—including lactic acid bacteria, bifidobacteria, and yeasts—employed in agri-food fermentations, their functional roles in bioactive compound production and digestibility improvement, and the integration of prebiotic substrates from agricultural sources into synbiotic formulations that enhance probiotic viability and functionality. Enzyme-assisted fermentation technologies are critically examined, including the roles of exogenous and endogenous carbohydrates, proteases, and phytases in substrate modification, reduction of anti-nutritional factors, and liberation of bioactive metabolites. The synergistic mechanisms underlying enzyme–microbe interactions, wherein enzymatic pretreatment enhances substrate accessibility for subsequent microbial transformation, are analyzed in the context of process optimization and industrial implementation. Major applications are explored across functional dairy and plant-based alternatives, cereal and legume fermentations, fermented beverages and nutraceutical products, and integration with circular bioeconomy models for waste valorization. The review further addresses sustainability, safety, and regulatory considerations, including food safety assurance, shelf-life extension, environmental sustainability metrics, and policy frameworks governing novel fermentation products. Key challenges including probiotic viability standardization, synbiotic formulation stability, cost considerations, and scalability are evaluated alongside future directions integrating digital and precision fermentation technologies. By synthesizing current scientific knowledge and identifying strategic research pathways, this paper concludes that the integration of probiotic, synbiotic, and enzyme-assisted fermentation represents a pivotal strategy for developing nutritionally enhanced, sustainably produced, and functionally superior foods capable of addressing global food security and public health challenges.