Abstract Background This systematic review and meta-analysis were done to assess the incidence of nutritional complications at follow-up after one-anastomosis gastric bypass (OAGB) and Roux-en-Y gastric bypass (RYGB). Methods A systematic review and meta-analysis were carried out involving studies that compared the nutritional complications of Roux-en-Y gastric bypass (RYGB) and one-anastomosis gastric bypass (OAGB); these included the incidence of malnutrition as well as deficiencies of other nutritional elements, such as total protein, albumin, calcium, and iron. A comprehensive search strategy was implemented in PubMed, Embase, and the Cochrane Library. Effect sizes included the pooled odds ratios (ORs) and 95% confidence intervals (95% CIs), as well as mean differences (MDs) and 95% CIs of the percentage total weight loss (%TWL) and excess weight loss percentage (%EWL). Results Thirteen studies were included (12,964 patients, 66.27% females, 53.82% underwent OAGB). At the longest follow-up period (≥3 years), OAGB was associated with significantly higher %TWL (MD=5.41%, 95%CI, 1.52 to 9.29) and %EWL (MD=13.81%, 95%CI, 9.60 to 18.02) compared to RYGB. However, OAGB procedures were associated with malnutrition (OR=3.00, 95%CI, 1.68 to 5.36, p<0.0001), hypoalbuminemia (OR=2.38, 95%CI, 1.65 to 3.43, p<0.0001), hypoproteinemia (OR=1.85, 95%CI, 1.09 to 3.14, p=0.022), anemia (OR=1.38, 95%CI, 1.08 to 1.77, p=0.011), and hypocalcemia (OR=1.78, 95%CI, 1.01 to 3.12, p=0.046). On subgroup analyses, the proportions of anemia and hypoalbuminemia remained significantly higher at longer follow-up periods and in studies published in Asia. Conclusions Despite the favorable weight loss profile, the unfavorable nutritional consequences of OAGB merit further investigations to explore the malabsorptive element, ethnic variation, and the role of the biliopancreatic limb length.