Background: Type 2 diabetes is a common metabolic disorder in the world, and it has become a challenge for the health system. Some studies have indicated the desirable effects of synbiotics on metabolic factors in patients with diabetes. Aim: This study aimed to determine the effect of synbiotic supplementation on metabolic factors and systemic inflammation in patients with type 2 diabetes mellitus. Methods: In this randomized, double-blind controlled trial, 50 patients with type 2 diabetes randomly allocated to the synbiotic (containing Bacillus coagulans + Lactobacillus rhamnosus + Lactobacillus acidophilus and fructooligosaccharide) or placebo groups to received one sachet daily for 12 weeks. Glycemic index, Lipid profile, and hs-CRP measured at the beginning of the study and the end of the 12th week. Results: After 12 weeks, supplementation means a change of Hip circumference (HC) significantly decreased in the synbiotic group compared to the placebo group (-0.85±1.89 vs. 1.23±3.98). Although systolic blood pressure (SBP) and diastolic blood pressure (DBP) at the end of trial declined in the synbiotic group compared to baseline, respectively p=0.03, p=0.01. Analysis of covariance demonstrated that synbiotic supplementation during 12 weeks significantly reduced glycemic factors including fasting blood glucose (FBG), insulin, homeostatic Model Assessment for Insulin Resistance (HOMA-IR), β-cell function (HOMA-β) (p<0.05) and inflammatory index, hs-CRP (p<0.05) compared to placebo. Conclusion: The current study indicated Synbiotic supplementation could improve glycemic index, systemic inflammation and blood pressure in patients with type 2 diabetes. So correcting the intestinal microbial flora can be a new therapeutic approach to treating this disease. Trial registration: IRCT, IRCT20100524004010N27. Registered 7 January 2019, https://www.irct.ir/trial/36535