Abstract Background Laparoscopic Roux-en-Y gastric bypass (LRYGB) and laparoscopic sleeve gastrectomy (LSG) are associated with glucose metabolism improvement although data on insulin resistance remission rates after these procedures are lacking. Aims Primary aim was to compare insulin resistance remission rates achieved after LRYGB and LSG, using population-specific HOMA-IR cut-off points. Secondary objectives were to analyze factors associated with type 2 diabetes mellitus (T2DM) complete remission according to the new American Diabetes Association criteria and to examine changes in HOMA-B during follow-up. Methods Non-randomized, prospective cohort study of patients undergoing LRYGB or LSG with a minimal follow-up of 24 months. Patients on insulin therapy were excluded. Results At baseline, 56 (48.7%) of the 115 LRYGB group and 48 (61.5%) of the 78 LSG group had insulin resistance, and 29 (25.2%) and 20 (25.6%) T2DM, respectively. No differences were detected in insulin resistance remission rate (92.9% LRYGB and 87.5% LSG, p = 0.355) nor in T2DM complete remission at 2 years (62.1 vs 60% respectively, p = 0.992). Factors independently associated with T2DM complete remission were diabetes treatment and a greater decrease in 3-month HOMA-IR index. The HOMA-B index showed a progressive decline during follow-up. Conclusion Both surgical techniques are equally effective in achieving insulin resistance normalization in the majority of severely obese patients. Three-month HOMA-IR reduction after surgery was the main predictor of T2DM complete remission.