This systematic review aimed to compile various research designs, including experimental, longitudinal, cross-sectional, and case studies in humans and experimental studies in rodents, to examine changes in Akkermansia muciniphila abundance in response to exercise. This comprehensive approach can improve our understanding of A. muciniphila response to physical exercise and highlight gaps in the literature, providing valuable insights for future microbiome research. Four databases (Web of Science, PubMed, Scopus, and Sports Discuss) were searched in the literature. Quality assessment was conducted independently and in duplicate using two risk-of-bias tools (Downs and Black for human studies and SYRCLE's risk of bias for animal studies). 3,901 studies were identified, with thirteen human studies and nine animal studies included after screening. Of the thirteen human studies analysed, five (38.5%) were cross-sectional, seven (53.8%) were longitudinal/experimental, and one (7.7%) was a case study. These studies included 522 participants, among whom 157 were athletes, such as rugby players, marathon runners, triathletes, and skiers. Six studies reported an increase in A. muciniphila, five showed a decrease, and two found no significant differences. Regarding interventions, two studies used a combination of moderate-intensity strength and aerobic training, while seven used low to moderate-intensity aerobic exercises. In the nine rodent studies, eight (88.9%) were conducted on mice and one (11.1%) on rats, with all being experimental. These studies involved 310 animals. Eight studies reported a substantial increase in A. muciniphila, while one found no differences. Among these, eight employed moderate-intensity aerobic exercises as the intervention, and one utilised low-to-moderate-intensity strength training. The studies summarised in this review indicate that the impact of various physical exercise protocols on A. muciniphila abundance in humans remains controversial. However, rodent studies provide strong evidence that aerobic exercise increases A. muciniphila abundance in faecal pellets of both healthy and diseased models.