Aerobic exercise alters gut microbiome composition, yet the impact of gentle physiotherapy on gut microbiome and its relation to muscle strengthening and physical function remains unexplored. Physiotherapy exercises modulate gut microbiome composition and changes in gut microbes are linked to improvements in muscle strength or function. Secondary data analysis of samples from a randomized controlled trial. Level 2b. Data from a 6-week randomized controlled trial of physiotherapy for knee pain were analyzed. Gut microbiota profiling utilized 16S sequencing. We compared intervention and control (usual care) groups using microbial diversity metrics. Amplicon sequence variants (ASVs) that changed after the program were identified with ALDEX2, and correlations between these ASVs and measures of physical function, muscle strength, and interleukin-6 (IL-6) were explored. No diversity changes were observed between standard care (n = 43) and physiotherapy (n = 34). Physiotherapy led to significant increases in Alistipes, Bacteroides, Clostridium sensu stricto 1, and Faecalibacterium ASVs. Of these, Clostridium sensu stricto 1 and Faecalibacterium were associated with postintervention muscle strength. Increase in Faecalibacterium was correlated with a decrease in IL-6 in the physiotherapy group. Physiotherapy had modest effects on gut microbiome composition affecting 4 taxa. Increases in muscle strength were correlated with increases in 2 taxa including Faecalibacterium. Faecalibacterium was also linked to reduced inflammation. Improved walking speed was linked to an increase in Alistipes with no differences found for strength or squatting ability. Improved gut microbiome composition is linked to better overall health outcomes, including enhanced immune function, reduced inflammation, and improved metabolic health. This is particularly relevant for patients with osteoarthritis, who are known to have a high prevalence of cardiometabolic comorbidities. Integrating physiotherapy protocols that positively influence the gut microbiome can thus enhance overall patient outcomes.