Exercise induces many health benefits, preventing or treating diseases. On the other hand, the intestine houses trillions of microbes with the ability to influence the normal physiology of the organism. The intestinal microbiota is immensely diverse, varies between individuals, and can fluctuate according to various factors, including physical activity. In this sense, the aim of this systematic review is to search through the recent knowledge, in order to elucidate the roles played by different exercise modalities on modulation of the intestinal microbiota of adults. A literature search was performed in the PubMed, SCOPUS and Web of Science databases. The main inclusion criteria were randomised controlled trials involving exercise and microbiota in adults. The initial search identified 1,103 publications of which 13 were finally included. The heterogeneity of the training parameters used in the studies, statistical analyses, and sequencing methods did not allow us to carry out a meta-analysis. However, the results tend to show that modulation of the gut microbiome is related to the type of exercise, the intensity and the time of intervention, where these changes are more significant at the level of specific microbial populations than richness and diversity indices.