Here, we propose an easy method for site-selective deposition of two-dimensional (2D) material flakes onto nanoholes by means of electrophoretic deposition. This method can be applied to both simple flat nanostructures and complex three-dimensional structures incorporating nanoholes. The deposition method is here used for the decoration of large ordered arrays of plasmonic structures with either a single or few layers of MoS2. In principle, the plasmonic field generated by the nanohole can significantly interact with the 2D layer leading to enhanced light-material interaction. This makes our platform an ideal system for hybrid 2D material/plasmonic investigations. The engineered deposition of 2D materials on plasmonic nanostructures is useful for several important applications such as enhanced light emission, strong coupling, hot-electron generation, and 2D material sensors.