ObjectiveThis systematic review and meta-analysis study aimed to evaluate the effectiveness of probiotics supplementation on glycaemic control in patients with type 2 diabetes mellitus (T2DM) based on the data from the randomised clinical trials (RCTs).MethodsPubMed, Web of Sciences, Embase, and Cochrane Library were searched from the inception to October 2022, and RCTs about probiotics and T2DM were collected. The standardised mean difference (SMD) with 95% confidence interval (CI) was used to estimate the effects of probiotics supplementation on glycaemic control related parameters, e.g. fasting blood glucose (FBG), insulin, haemoglobin A1c (HbA1c), and homeostasis model of assessment of insulin resistance (HOMA-IR).ResultsThirty RCTs including 1,827 T2MD patients were identified. Compared with the placebo group, the probiotics supplementation group had a significant decrease in the parameters of glycaemic control, including FBG (SMD = − 0.331, 95% CI  − 0.424 to − 0.238,Peffect< 0.001), insulin (SMD = − 0.185, 95% CI  − 0.313 to − 0.056,Peffect= 0.005), HbA1c (SMD = − 0.421, 95% CI  − 0.584 to − 0.258,Peffect< 0.001), and HOMA-IR (SMD = − 0.224, 95% CI  − 0.342 to − 0.105,Peffect< 0.001). Further subgroup analyses showed that the effect was larger in the subgroups of Caucasians, high baseline body mass index (BMI ≥ 30.0 kg/m2),Bifidobacteriumand food-type probiotics (Psubgroup< 0.050).ConclusionThis study supported that probiotics supplementation had favourable effects on glycaemic control in T2DM patients. It may be a promising adjuvant therapy for patients with T2DM.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12967-023-04306-0.