The emergence of next-generation functional foods marks a transformative shift in the intersection of nutrition science, microbiology, and personalized healthcare. These advanced food formulations are designed to modulate the gut microbiota—a complex and dynamic microbial ecosystem that plays a central role in metabolic, immune, and neurological functions. By leveraging cutting-edge technologies such as microbiome profiling, next-generation sequencing, and bioinformatics, functional foods can now be tailored to individual microbiota compositions. This personalized approach enables targeted dietary interventions to prevent and manage chronic diseases, optimize nutrient absorption, and enhance overall well-being. Despite challenges in regulation, standardization, and consumer engagement, next-generation functional foods offer significant promise as tools for precision nutrition and integrative health management.