Introduction: Recent progress has been made to gut microbiota, regenerative nutrition and skeletal muscle metabolism. In this context, regular physical training associated with nutrological health has broad benefits for the health of the intestinal microbiota. The triad physical exercise, nutrition and intestinal microbiota for the process of muscle regeneration, adult stem cells stand out as gut stem cells. Objective: the present study aimed to carry out a systematic review on the main cellular and molecular aspects of regenerative nutrition in the modulation of the intestinal microbiota and the metabolism of skeletal muscle. Methods: The rules of the Systematic Review-PRISMA Platform. The research was carried out from June 2021 to January 2022 and developed based on Scopus, PubMed, Science Direct, Scielo, and Google Scholar. The quality of the studies was based on the GRADE instrument and the risk of bias was analyzed according to the Cochrane instrument. Results and Conclusion: A total of 215 studies were analyzed, with only 32 medium and high-quality studies selected, according to the rules of the GRADE, and with bias risks that do not compromise scientific development, based on the Cochrane instrument. A current focus in the field of sport and metabolism is the investigation of how specific metabolites and nutrients affect the progression and treatment of muscle injuries. Nutrients can also regulate normal homeostatic processes, altering the decisions of muscle stem cells and satellites. Thus, the implications for understanding how diet influences cellular transitions are immense and will guide precision-based nutrition to improve overall health and therapeutic strategies for muscle injuries. Thus, metabolic pathways and chromatin modifications are closely linked, and hence many changes in metabolism influence epigenetic changes and alter gene expression. For example, signaling pathways including mTORC, AMPK, MAPK, and others are all sensitive to changes in nutrient levels.