Introduction There are several randomised controlled trials (RCTs) that have already shown that metabolic/bariatric surgery achieves short-term and long-term glycaemic control while there are no level 1A of evidence data regarding the effects of surgery on the microvascular complications of type 2 diabetes mellitus (T2DM).

Purpose The aim of this trial is to investigate the long-term efficacy and safety of the Roux-en-Y gastric bypass (RYGB) plus the best medical treatment (BMT) versus the BMT alone to improve microvascular outcomes in patients with T2DM with a body mass index (BMI) of 30–34.9 kg/m2.

Methods and analysis This study design includes a unicentric randomised unblinded controlled trial. 100 patients (BMI from 30 to 34.9 kg/m2) will be randomly allocated to receive either RYGB plus BMT or BMT alone. The primary outcome is the change in the urine albumin-to-creatinine ratio (uACR) captured as the proportion of patients who achieved nephropathy remission (uACR<30 mg/g of albumin/mg of creatinine) in an isolated urine sample over 12, 24 and 60 months.

Ethics and dissemination The study was approved by the local Institutional Review Board. This study represents the first RCT comparing RYGB plus BMT versus BMT alone for patients with T2DM with a BMI below 35 kg/m2.