Abstract The creation of SERS‐active substrates is investigated by self‐assembling hierarchical structures of plasmonic‐assisted nanospheres (HSNs). The hierarchical architecture exploits the advantages of the well‐known ordered configuration of a hexagonally closed‐packed array (CPA) of nanospheres. A further layer of upper nanospheres is used to provide regular and intense surface hotspots, located at the nanogaps between neighboring nanospheres. Numerical analysis is carried out to predict the SERS performances and to identify the more promising configurations, by offering design criteria and a physical insight on the conditions affecting the SERS response of the self‐assembled substrates. Two alternative self‐assembly fabrication methods have been pursued to realize HSNs, namely co‐deposition and sequential deposition. Morphological analysis revealed the formation of well‐ordered hierarchical structures with different ratios between the diameters of the bottom and upper nanospheres. Experimental analysis of the SERS response demonstrates that HSNs can work as cost‐effective SERS substrates with superior performances with respect to the simpler single‐layer CPA configurations.