Abstract Introduction The comparison of effectiveness between R-en-Y gastric bypass (RYGB) and one anastomosis gastric bypass (OAGB/MGB) remains unclear, as well as the changes in gut microbiota (GM). Materials: prospective, cohort, multi-centre study enrolling 96 patients with severe obesity, applying inclusion criteria, randomised between OAGB/MGB or RYGB. Faecal and blood samples were collected, pre- (T0) and 12 months postoperatively (T1). GM was determined by V3-V4 16S rRNA regions sequencing and home-made bioinformatic pipeline based on Qiime2 plugin and R packages. A standardised meal test was performed at T0 and T1 with 250 ml of liquid meal Oxepa (Abbott, Japan). Aim To evaluate and compare OAGB/MGB vs RYGB microbiota profile shift postoperatively and its impact on metabolic and nutritional status. Results 54 patients completed the study, 27 for each procedure (females 61%). No significant differences were found at T0 for anthropometric and nutritional parameters, while a statistically significant anthropometrics’ reduction was registered at T1, with a significant improvement of glucose and lipid profile, and significant reduction in vitamins and iron. Postoperatively fasting glucose, lipid profile, vitamins and minerals were not significantly different between the 2 procedures. Fasting GLP-1 was higher at T1, but postprandial values showed a lower peak both 60' and 120' after ingestion of the mixed meal., with no significant difference between the 2 groups. Examining the GM’s alpha and beta diversity, Firmicutes/Bacteroides ratio increased postoperatively, mainly dependent on Bacteroidetes decreasing. Relative abundances evaluation highlighted those main differences between the identified clusters (group A 29 subjects, group B 14 subjects and group C 10 subjects) were dependent on variation in Bacteroidetes and Firmicutes. A different trend was detected at Phylum level between T0 and T1 of each cluster. Bacteroides and Streptococcus genera appeared mainly changed between the three groups (both showing p< 0.001). Conclusions The emergence of slightly different GM profile postoperatively may be related to clinical condition or may play a key role in the long-term outcome and may represent a biomarker to follow bariatric surgery’s outcomes. No difference between the two bypass techniques were found in GM profile or other examined metabolic parameters one year postoperatively.