In this review, we searched for clinical and experimental studies related to acupuncture-related therapy (ART) on the microbiome in musculoskeletal disorders (MSDs) through the electronic databases of MEDLINE via PubMed, EMBASE, and Oriental Medicine Advanced Searching Integrated System up to May 2023, without language restriction, and after the selection/exclusion process, the study design, target disease, intervention details, treatment period, outcomes, and study results were extracted. A total of 8 articles were selected. Two randomized controlled trials and 6 animal studies evaluated knee osteoarthritis, rheumatoid arthritis, spinal cord injury, ankylosing spondylitis, and osteoporosis. ART, including electroacupuncture, thread-embedding acupuncture, and moxibustion, affected microbiome modulation in MSDs. The results reveal that ART could be a potential treatment for regulating the microbiome in MSDs. However, further high-quality studies are needed.