A systematic review and meta-analysis of the effects of physical activity (PA) and sedentary behavior (SB) on the human microbiome was conducted, including 91 studies with 2632 participants. The results showed no consistent effect of PA on microbial alpha-diversity, although there was a trend toward higher microbial richness in athletes compared to non-athletes. PA was associated with increased abundance of short-chain fatty acid (SCFA)-producing bacteria such as Akkermansia, Faecalibacterium, Veillonella, and Roseburia. SB had limited evidence of effect on the microbiome. The studies showed high heterogeneity, making it difficult to draw conclusive information about the role of PA and SB in microbial composition. Future multi-omics studies are needed to better understand the molecular effects of PA and SB on the microbiome. The review highlights the need for well-designed studies using objective measures like accelerometry to assess PA and SB, and for multi-omics approaches to explore the functional aspects of the microbiome in response to PA and SB. The findings suggest that PA may positively influence the microbiome, particularly in athletes, but more research is needed to clarify the mechanisms and effects of PA and SB on the microbiome.A systematic review and meta-analysis of the effects of physical activity (PA) and sedentary behavior (SB) on the human microbiome was conducted, including 91 studies with 2632 participants. The results showed no consistent effect of PA on microbial alpha-diversity, although there was a trend toward higher microbial richness in athletes compared to non-athletes. PA was associated with increased abundance of short-chain fatty acid (SCFA)-producing bacteria such as Akkermansia, Faecalibacterium, Veillonella, and Roseburia. SB had limited evidence of effect on the microbiome. The studies showed high heterogeneity, making it difficult to draw conclusive information about the role of PA and SB in microbial composition. Future multi-omics studies are needed to better understand the molecular effects of PA and SB on the microbiome. The review highlights the need for well-designed studies using objective measures like accelerometry to assess PA and SB, and for multi-omics approaches to explore the functional aspects of the microbiome in response to PA and SB. The findings suggest that PA may positively influence the microbiome, particularly in athletes, but more research is needed to clarify the mechanisms and effects of PA and SB on the microbiome.