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Herein we report a selective DIBAL-H-mediated reduction of a heterocyclic diester to the corresponding monoaldehyde using continuous flow chemistry. The use of continuous flow enabled operation at lower temperatures and better control of the reaction time, thereby allowing for a significant increase in reaction selectivity and yield compared with batch conditions. The reaction’s development as a continuous flow process and its scale-up from laboratory gram scale to multikilogram scale are discussed, including design of experiments studies to probe the optimal reaction window.