A clean and efficient protocol for the synthesis of a wide variety of N-Boc-beta-amino ketones 3a-g has been defined using flow approach. The multistep procedure is based on the beta-azidation of unsaturated ketones, consecutive reduction of the azido group, and concomitant amino group protection, and furnishes the desired products in good yields and very low E-factors ranging from 3.1 to 5.6. In batch conditions and by water as reaction medium, poorer yields and complicated reaction mixtures are obtained. Adoption of the flow approach, which combines transformations performed in solvent-free conditions and in EtOAc, has been essential in order to avoid side reactions, poisoning of the reduction catalyst, and use of minimal amount of reactants.