Algae‐derived natural compounds have shown significant potential in treating various health conditions, including cancer, obesity, diabetes, and inflammation. Recent advancements in nanotechnology have enabled the development of precise drug delivery systems and diagnostic tools utilizing these compounds. Central to this innovation are the vibrant pigments found in algae chlorophylls, carotenoids, and phycobiliproteins which not only impart color but also possess notable nutritional, medicinal, and antioxidant properties. These pigments are extensively used in supplements and the food industry for their health benefits. Emerging research highlights the role of algal pigments in promoting gut health by modulating gut microbiota. This review comprehensively examines the therapeutic benefits of algae, recent progress in algal‐derived nanoparticle technology, and the synergistic effects of algae and their pigments on gut health. Novel insights and recent data underscore the transformative potential of algal compounds in modern medicine and nutrition.