Internal herniation (IH) is a common problem after laparoscopic Roux-en-Y gastric bypass surgery (RYGB). Routine closure of the mesenteric defects (MDs) reduces the risk of IH. Only very few articles report on risk factors for IH or describe detailed closing techniques. There is no consensus yet on the best closing method. The objective of this study is to determine the optimal stapling method for closure of MDs after RYGB. All performed RYGB procedures in our high-volume bariatric institute were included. Quality of the closure was scored in the categories poor, sub-optimal, and optimal, to see if the quality of the closure would predict the chance of reopening of the MDs and, therefore, the chance of IH. During any type of laparoscopy in the follow-up of the patient, the conditions of the MDs were stated, for example during diagnostic laparoscopy in symptomatic patients suspicious for IH or during laparoscopic cholecystectomy. Technically well-executed closure of Petersen’s space (PS) with two rows of staples had a greater chance of still being closed upon re-inspection compared to closure with one row (odds ratio = 8.1; 95% confidence interval [1.2–53.2], p = 0.029). Optimal closure of the MD at the jejuno-jejunostomy (JJ-space, JJS) resulted in more closed JJSs upon re-inspection compared to sub-optimal closure (odds ratio = 3.6 [CI 95% 0.8–16.1], p = 0.099). Non-optimally closed MDs had higher reopening rates and, therefore, pose an additional risk for IH. Our classification provides a quality assessment of MD closure during RYGB and gives insight into how to optimize surgical technique.