We report an enzyme‐catalyzed dynamic kinetic resolution protocol for the one‐pot asymmetric synthesis of substituted purine derivatives with high product yield (up to 96%) and enantio purity (up to 99%). The controllable N‐9/N‐7 substitution, which posed formidable challenges in organic synthesis, could be accomplished by choosing different types of enzymes as the catalyst. This method was proved easily scalable and was successfully used to prepare a series of prodrugs of medicinally active acids. In addition, the biocatalysts exhibited good recyclability, indicating the potential of this strategy for practical applications in the pharmaceutical industry.