Noni (Morinda citrifolia L.) is a tropical fruit rich in bioactive compounds. Little is known about its polyphenol composition at different ripeness levels and digestive characteristics. Here, we studied changes in polyphenols and antioxidant activity as noni ripened. Rutin and kaempferol-3-O-rutinoside were found in high amounts in noni, with antioxidant capacity increasing as it ripened. Under simulated digestion, polyphenols were gradually released from the oral to gastrointestinal phases, partially decomposing in the small intestine due to their instability. Conversely, fiber-bound phenols were released during colonic fermentation, leading to high bioaccessible antioxidant activity. Additionally, noni consumption affected the intestinal microbiome by reducing the Firmicutes/Bacteroidetes ratio and increasing bacteria with prebiotic properties like Prevotella and Ruminococcus. These findings demonstrate that polyphenols significantly contribute to the health benefits of noni fruit by providing absorbable antioxidants and improving the structure of the intestinal microbiome.