Background It has been suggested that shortening the length of the biliopancreatic limb (BPL) to 150 cm in one anastomosis gastric bypass (OAGB) would reduce nutritional complication rates without impairing weight loss outcomes. The aim of this study is to compare patients who underwent OAGB with a 200-cm BPL (OAGB-200) to patients with OAGB with a 150-cm BPL (OAGB-150) in terms of weight loss and late morbidity. Methods This is a monocentric retrospective matched cohort study including patients with a body mass index between 35 and 50 kg/m2 who underwent an OAGB-150 or an OAGB-200. Patients were matched 1:1 based on age, sex, and body mass index, prior to bariatric surgery. Results In total, 784 patients who underwent OAGB were included (OAGB-150 n = 392 and OAGB-200 (n = 392). There was no significant difference in terms of early morbidity. Regarding late morbidity in patients with an OAGB-150, significantly lower rates for marginal ulcer (OR = 0.4, CI 95% [0.2; 0.8], p = 0.006), incisional hernia (OR = 0.5, CI 95% [0.3; 1], p = 0.041), and bowel obstruction (OR = 0.3, CI 95% [0.1; 0.9], p = 0.039) were reported. Likewise, regarding late nutritional deficiencies, post-OAGB-150, a significantly lower number of patients with hypoalbuminemia (OR = 0.3, CI 95% [0.2; 0.7], p = 0.006), low vitamin B9 (OR = 0.5, CI 95% [0.2; 1], p = 0.044), and low ferritin (OR = 0.5, CI 95% [0.3; 0.8], p = 0.005) were observed. There was no significant difference in the percentage of excess BMI loss at 1, 2, 3, 4, and 5 years. Conclusion Compared to OAGB-200 in patients with BMI ≤ 50 kg/m2, OAGB-150 results in fewer nutritional deficiency rates long term, without impairing weight loss.