The poly cystic ovary syndrome (PCOS) is a highly common endocrine-metabolic condition in women of reproductive age, which involves insulin resistance, hyperandrogenism, and ovulatory malfunction. According to new evidence, there is an involvement of gut microbiota in the pathophysiology of PCOS, and microbiomeoriented therapies are attracting great attention. This systematic review identifies the effectiveness of probiotics, prebiotics and synbiotics in the management of insulin resistance and hormonal dysregulation in women with PCOS, using the randomized clinical trial (RCTs). A large scale of electronic databases was searched to identify relevant RCTs considering metabolic, endocrine outcomes in the context of the microbiome-modulating intervention. It was shown that the markers that probiotic and synbiotic supplementation substantially increased include fasting insulin, HOMA-IR, total testosterone, LH/FSH ratio, and menstrual regularity. Prebiotics were less well studied and had promise. Some of the suggested mechanisms are regulating gut dysbiosis, supporting short-chain fatty acid production, systemic inflammation, and intestinal barrier performance. Although promising, heterogeneity in the study designs, strains, dosage, and treatment duration does not allow making firm conclusions. Additional good-quality, long-term RCTs are needed to validate treatment worth and come up with standard guidelines. However, the introduction of microbiome-directed interventions can be viewed as a new adjunctive approach to metabolic and reproductive outcomes in PCOS in females.