This systematic review and meta-analysis examines the effects of physical activity (PA) and sedentary behavior (SB) on the human microbiome across different body sites and populations. The study included 91 studies, primarily cross-sectional, with a focus on healthy individuals. The meta-analyses of 2632 participants revealed no consistent effect of PA on microbial alpha-diversity, although there was a trend toward higher microbial richness in athletes compared to non-athletes. Active individuals showed an increase in short-chain fatty acids (SCFAs)-producing bacteria such as *Akkermansia*, *Faecalibacterium*, *Veillonella*, and *Roseburia*. The review highlights the need for more well-designed, multi-omics studies to enhance understanding of the molecular mechanisms underlying the effects of PA and SB on the microbiome.This systematic review and meta-analysis examines the effects of physical activity (PA) and sedentary behavior (SB) on the human microbiome across different body sites and populations. The study included 91 studies, primarily cross-sectional, with a focus on healthy individuals. The meta-analyses of 2632 participants revealed no consistent effect of PA on microbial alpha-diversity, although there was a trend toward higher microbial richness in athletes compared to non-athletes. Active individuals showed an increase in short-chain fatty acids (SCFAs)-producing bacteria such as *Akkermansia*, *Faecalibacterium*, *Veillonella*, and *Roseburia*. The review highlights the need for more well-designed, multi-omics studies to enhance understanding of the molecular mechanisms underlying the effects of PA and SB on the microbiome.