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Abstract Objective The purpose of the present study was to evaluate the effectiveness of probiotics on type II diabetes mellitus (T2DM). Methods We performed a comprehensive search on PubMed, Web of Science, China National Knowledge Infrastructure, Chinese Scientific Journal Databases, Wan Fang database and China biology medicine disc for relevant studies published before June 2019. Glycated hemoglobin A1c (HbA1c), homeostasis model assessment of insulin resistance (HOMA-IR) and fasting blood glucose (FBG) were used as indicators for T2DM. Inverse-variance weighted mean difference (WMD) with 95% confidence interval (CI) was calculated for the mean HbA1c, FBG and HOMA-IR changes from baseline. Results 15 randomized controlled trials (RCT) with a total of 902 participants were included into the meta-analysis. Considering the clinical heterogeneity caused by variation of dosage and duration of probiotic treatment, random-effects model was used to estimate the pooled WMD. Significantly greater reduction in HbA1c% (WMD = − 0.24, 95% CI [− 0.44, − 0.04], p = 0.02), FBG (WMD = − 0.44 mmol/L, 95% CI [− 0.74, − 0.15], p = 0.003) and HOMA-IR (WMD = − 1.07, 95% CI [− 1.58, − 0.56], p |