Skeletal muscle plays a vital role in the conversion of chemical energy into physical force. Muscle atrophy, characterized by a reduction in muscle mass, is a symptom of chronic disease (cachexia), aging (sarcopenia), and muscle disuse (inactivity). To date, several trials have been conducted to prevent and inhibit muscle atrophy development; however, few interventions are currently available for muscle atrophy. Recently, food ingredients, plant extracts, and phytochemicals have received attention as treatment sources to prevent muscle wasting. Flavonoids are bioactive polyphenol compounds found in foods and plants. They possess diverse biological activities, including anti-obesity, anti-diabetes, anti-cancer, anti-oxidation, and anti-inflammation. The effects of flavonoids on muscle atrophy have been investigated by monitoring molecular mechanisms involved in protein turnover, mitochondrial activity, and myogenesis. This review summarizes the reported effects of flavonoids on sarcopenia, cachexia, and disuse muscle atrophy, thus, providing an insight into the understanding of the associated molecular mechanisms.