Metallic nanoparticles (MNPs) and metallic nanostructures are both commonly used, independently, as SERS substrates due to their enhanced plasmonic activity. In this work, we introduce and investigate a hybrid nanostructure with strong SERS activity that benefits from the collective plasmonic response of the combination of MNPs and flow-through nanohole arrays (NHAs). The electric field distribution and electromagnetic enhancement factor of hybrid structures composed of silver NPs on both silver and gold NHAs are investigated via finite-difference time-domain (FDTD) analyses. This computational approach is used to find optimal spatial configurations of the nanoparticle positions relative to the nanoapertures and investigate the difference between Ag-NP-on-Ag-NHAs and Ag-NP-on-Au-NHAs hybrid structures. A maximum GSERS value of 6.8 × 109 is achieved with the all-silver structure when the NP is located 0.5 nm away from the rim of the NHA, while the maximum of 4.7 × 1010 is obtained when the nanoparticle is in full contact with the NHA for the gold-silver hybrid structure. These results demonstrate that the hybrid nanostructures enable hotspot formation with strong SERS activity and plasmonic enhancement compatible with SERS-based sensing applications.