The gut microbiota is a complex heterogeneous microbial community modulated by endogenous and exogenous factors. Among the external causes, nutrition as well as physical activity appear to be potential drivers of microbial diversity, both at the taxonomic and functional level, likely also influencing endocrine system, and acting as endocrine organ itself. To date, clear-cut data regarding which microbial populations are modified, and by which mechanisms are lacking. Moreover, the relationship between the microbial shifts and the metabolic practical potential of the gut microbiota is still unclear. Further research by longitudinal and well-designed studies is needed to investigate whether microbiome manipulation may be an effective tool for improving human health and, also, performance in athletes, and whether these effects may be then extended to the overall health promotion of general populations. In this review, we evaluate and summarize the current knowledge regarding the interaction and cross-talks among hormonal modifications, physical performance, and microbiota content and function.