The production of coenzyme B-12 using well-characterized microorganisms, such as Escherichia coli, has recently attracted considerable attention to meet growing demands of coenzyme B-12 in various applications. In the present study, we designed an auxotrophic selection strategy and demonstrated the enhanced production of coenzyme B-12 using a previously engineered coenzyme B-12-producing E. coli strain. To select a high producer, the coenzyme B-12-independent methionine synthase (metE) gene was deleted in E. coli, thus limiting its methionine synthesis to only that via coenzyme B-12-dependent synthase (encoded by metH). Following the deletion of metE, significantly enhanced production of the specific coenzyme B-12 validated the coenzyme B-12-dependent auxotrophic growth. Further precise tuning of the auxotrophic system by varying the expression of metH substantially increased the cell biomass and coenzyme B-12 production, suggesting that our strategy could be effectively applied to E. coli and other coenzyme B-12-producing strains.