Background: Management of vitamin B12 (cobalamin, Cbl) deficiency in inflammatory bowel disease (IBD) is often not evidenced-based because of uncertainty on whether it causes enough malabsorption to result in clinical disease. This systematic review examines whether IBD predisposes to Cbl deficiency. We provide an approach to the management of abnormal Cbl values in IBD based on current literature and consensus-based guidelines. Methods: An extensive search of the Ovid MEDLINE and EMBASE databases by independent reviewers identified 42 articles with a total of 3732 patients evaluating Cbl deficiency in IBD. Results: Crohn's disease without ileal resection, regardless of disease location in the ileum, did not increase the risk for Cbl deficiency. Ileal resections greater than 30 cm were associated with Cbl deficiency in Crohn's disease, whereas those less than 20 cm were not. The effects of 20 to 30 cm resections were inconsistent. Ulcerative colitis did not predispose to deficiency. All studies failed to use confirmatory biomarker testing as stipulated by diagnostic guidelines for Cbl deficiency. Conclusions: This literature does not support an association of Crohn's disease in general, regardless of ileal involvement, with Cbl deficiency. Only ileal resections greater than 20 cm in Crohn's disease predispose to deficiency and warrant treatment. Based on these findings, we suggest a diagnostic and therapeutic algorithm. All findings and recommendations require verification in further studies using confirmatory biomarkers as per diagnostic guidelines for Cbl deficiency. Serum Cbl levels alone are likely insufficient to diagnose deficiency in asymptomatic patients.