Skeletal muscle is essential to human motor functions. The quantity and quality of skeletal muscle can flexibly change to adapt to several conditions, such as exercise, disease, and nutritional status. Declines in skeletal muscle mass or its function can contribute to heart disease, diabetes, obesity, and premature death. Therefore, it is important to maintain muscle mass and function. This chapter outlines functional food factors that can prevent skeletal muscle atrophy or enhance muscle mass. Specifically, flavonoids derived from plant-based foods are one of the promising food factors for preventing skeletal muscle atrophy. Quercetin (3,3′,4′,5,7-pentahydroxyflavone), an antioxidative flavonoid, has several beneficial effects on health owing to its antioxidative and anti-inflammatory properties. Research on quercetin suggests that mitochondrial function and antioxidative enzymes are the targets for preventing oxidative stress in muscle atrophy. As another example, hops (Humulus lupulus L.) is a source of prenylflavonoids, including 8-prenylnaringenin (8-PN). Studies have shown that 8-PN can suppress muscle atrophy by suppressing the expression of the muscle atrophy-related ubiquitin ligase MAFbx-1/atrogin-1 and enhancing protein kinase B phosphorylation in the muscle. In summary, maintaining muscle mass and function are crucial for human health, and flavonoids are functional food compounds that have anti-muscle atrophy effects.