This review examines how quinoa and its protein-derived peptides can improve gut health by changing the balance of bacteria in the digestive system. Research shows that quinoa helps boost beneficial bacteria, increases diversity of microbial communities, and promotes production of butyrate, a beneficial compound that supports intestinal health. Different disease conditions show specific improvements, such as reduced harmful bacteria in colitis and better metabolic balance in obesity, suggesting quinoa could be tailored for personalized health interventions.