Background Few investigations have been conducted that compared blood glucose in patients with diabetes mellitus (DM2) and morbid obesity who had undergone laparoscopic sleeve gastrectomy (LSG) or gastric bypass (LRYGB). We aimed to compare the effects of these procedures using continuous glucose monitoring (CGM). Methods We prospectively studied patients that had qualified for LSG or LRYGB. The inclusion criteria were DM2 of ≤ 5 years, for which patients were taking oral anti-diabetic drugs, or no glucose metabolism disorder; and morbid obesity. CGM was performed between admission and the 10th postoperative day. Results We studied 16 patients with DM2 and 16 without. Eighteen patients underwent LSG and 14 underwent LRYGB. The median hemoglobin A1c was 5.5% (5.4-5.9%) in DM2 patients, which did not differ from control (p = 0.460). Preoperative mean daily glucose concentration was similar between DM2 and control patients (p = 0.622). For patients with DM2, LRYGB was associated with more frequent low glucose status, and these episodes lasted longer than in DM2 patients that underwent LSG (p = 0.035 and 0.049, respectively). DM2 patients that underwent LRYGB demonstrated lower glucose concentrations from third postoperative day than those that underwent LSG. Patients without DM2 did not demonstrate differences in daily mean glucose concentrations, or in incidence nor duration of hypoglycemia throughout the observation period.Conclusion A significantly larger reduction in interstitial glucose concentration is present from third day in patients with DM2 who undergo LRYGB vs. LSG, accompanied by a lower incidence and shorter duration of low glucose episodes.