The synthesis of acyclic N4-substituted cytosine nucleoside phosphonates using a microwave-assisted N4-silylation-amination and olefin cross-metathesis as key assembly steps is described. The microwave-assisted silylation-amination is compared to a conventional heating protocol. While yields and purities of the coupling products were comparable under both conditions, microwave heating allows a significant acceleration of the reaction (from 48 h to 5 h).