•The effects of glucose-lowering drugs in patients with type 2 diabetes (T2D) are potentially mediated by gut microbiota, and these drugs may also directly influence microbiome composition.•It has not been ascertained whether either dapagliflozin or gliclazide influences microbiome composition in patients with T2D.•This study found that microbiome composition was not altered by either dapagliflozin or gliclazide treatment.•Thus, the metabolic effects of either treatment are not likely to be driven by changes in colonic microbiome composition. Patients with type 2 diabetes (T2D) are usually treated with (combinations of) glucose-lowering medication. The effects of these drugs can be influenced by intestinal microbiota and vice versa, as these drugs can also influence microbiome composition. However, as there is currently little clinical insight into this bug–drug interaction, our study aimed to evaluate the effects of 12-week treatment with the SGLT2 inhibitor dapagliflozin and sulphonylurea gliclazide on gut microbiome composition in T2D patients treated with metformin. A total of 44 patients were randomized to either dapagliflozin or gliclazide treatment for 12 weeks. At baseline and after 12 weeks, faecal samples and 24-h urine were collected. During study visits, anthropometric data were measured and blood samples drawn after an overnight fast. Microbiome composition was determined by 16S rRNA gene sequencing. Plasma glucose, insulin, HbA1c and urinary glucose excretion were measured using conventional methods. While dapagliflozin and gliclazide similarly improved glycaemic control, dapagliflozin reduced and gliclazide increased fasting insulin. Dapagliflozin also greatly increased urinary glucose excretion whereas gliclazide did not, while body mass index, fat mass percentage and waist circumference were reduced by dapagliflozin, but increased by gliclazide. However, neither treatment significantly affected either gut microbiome alpha diversity or composition and, after treatment, no associations were found between microbiome composition and other clinical parameters. Even though gliclazide and dapagliflozin have different metabolic actions in patients with T2D, neither treatment altered the faecal microbiome, thereby suggesting that the observed metabolic changes are not mediated by their effects on the microbiota.