Dietary nutrients are crucial for human health and the survival of gut microbes. Diet plays a central role in gut microbiota, as microbes rely on ingested nutrients for biological functions. Research highlights the connection between gut microbiota and exercise. Moderate and intense exercise are common in endurance training. Studies suggest gut microbiota may influence athlete health and performance. Athletes should consider dietary strategies like protein supplements, carbohydrate loading, probiotics, and prebiotics. The diverse gut microbiome of elite athletes produces key metabolites like short-chain fatty acids. A gut–muscle axis may exist, influencing muscle quality and gut biodiversity. This work summarizes current knowledge on diet, exercise, gut microbiota, and skeletal muscle.