Aims/hypothesis The aim was to conduct a systematic review and meta-analysis of randomised controlled clinical trials assessing the effect of probiotic, prebiotic or synbiotic supplementation on gut microbiota and glucose control and lipid levels in individuals with diabetes. Methods MEDLINE, EMBASE and the Cochrane Library were searched. The eligibility criteria for the studies was involvement of participants with a diagnosis of type 1 or type 2 diabetes. Metabolic outcomes (glucose control, insulinaemia, and lipid profile) of any probiotic, prebiotic or synbiotic supplementation related to modification of gut microbiota (prebiotics, probiotics and synbiotics) were analysed. We provided a narrative synthesis and meta-analysis of the findings on metabolic outcomes from the studies. Metabolic outcomes were extracted post-intervention and expressed as mean differences (MDs) and 95% CIs between treatment and comparator groups. We pooled the results using a random-effects meta-analysis. The meta-analysis was conducted using Review Manager (RevMan) software. Results After the removal of duplicates and ineligible studies, 5219 studies were retained for review of titles and abstracts. The number of articles was reduced to 130 by review, for which the full-text articles were obtained and reassessed, 38 of which were included in the final meta-analysis. Overall, the use of prebiotics, probiotics or synbiotics reduced HbA 1c levels, but did not reach the threshold for significance (−2.17 mmol/mol, 95% CI −4.37, 0.03; p = 0.05, [−0.20%, 95% CI −0.40 to 0.00; p = 0.05, I 2 = 66%]) and had no effect on LDL-cholesterol levels (−0.05 mmol/l; 95% CI −0.14, 0.05, p = 0.35, I 2 = 37%). However, their consumption decreased levels of fasting blood glucose (−0.58 mmol/l; 95% CI −0.86, −0.30; p < 0.01, I 2 = 60%), total cholesterol (−0.14 mmol/l; 95% CI −0.26, −0.02, p = 0.02, I 2 = 39%), triacylglycerols (−0.11 mmol/l; 95% CI −0.20, −0.02, p = 0.01, I 2 = 21%) and insulinaemia (−10.51 pmol/l; 95% CI −16.68,−4.33, p < 0.01, I 2 = 74%), and increased HDL-cholesterol levels (0.04 mmol/l; 95% CI 0.01, 0.07, p < 0.01, I 2 = 24%).