Aims: This study aims to investigate the role of gut microbiota in polycystic ovarian syndrome (PCOS) induction by monosodium glutamate (MSG) with the study of the protective effect of flaxseeds. Methods: 24 female rats were divided into three groups: Group 1: distilled water; Group 2: MSG; and Group 3: flaxseed + MSG. Finally, body and ovarian weights, HOMA-IR, plasma (gonadal hormones, triglycerides, HDL, LDL, adiponectin, TNF-α, IL-6, and lipopolysaccharides), intestinal (alkaline phosphatase, myeloperoxidase, Trimethylamine N-oxide, and free fatty acid receptor 2 gene expression), ovarian tissue (Silent Information Regulator 1 (SIRT1), reduced glutathione, and gene expression of mitogen activated protein kinase (AMPKα) and SIRT1) were determined. In addition, vaginal swaps, ovarian histopathology, and immunohistochemical staining of BCL2 and Bax were done. Results: MSG-induced insulin resistance, dyslipidemia, intestinal dysbiosis, ovarian oxidative stress, and inflammation through modulation of the AMPKα/SIRT1 pathway. On the other hand, flaxseed significantly prevented these findings. Conclusion: MSG-induced gut dysbiosis that predisposes to PCOS and ingestion of flaxseed can be considered a prospective protective agent against PCOS development.