Here we optimized the electrophoretic deposition process for the fabrication of WS2 plasmonic nanohole integrated structures. We showed how the conditions used for site-selective deposition influenced the properties of the deposited flakes. In particular, we investigated the effect of different suspension buffers used during the deposition both in the efficiency of the process and in the stability of WS2 flakes, which were deposited on an ordered arrays of plasmonic nanostructures. We observed that a proper buffer can significantly facilitate the deposition process, keeping the material stable with respect to oxidation and contamination. Moreover, the integrated plasmonic structures that can be prepared with this process can be applied to enhanced spectroscopies and for the preparation of 2D nanopores.