The interplay between functional foods and the immune system represents a burgeoning area of research with significant implications for health promotion. Functional foods, rich in bioactive compounds, have shown promising immune-modulating effects by influencing gut microbiota composition and activity. This review explores the mechanisms through which bioactive compounds in functional foods modulate the gut microbiota, enhancing immune function and overall health. Key bioactive compounds, such as polyphenols, prebiotics, probiotics, and dietary fibers, are examined for their roles in promoting beneficial gut microbiota and subsequent immunomodulation. The review also highlights recent studies demonstrating the potential of functional foods to prevent and manage various health conditions through gut microbiota modulation and immune support. Understanding these interactions offers valuable insights into the development of dietary strategies aimed at enhancing immune health and preventing disease.